diff --git a/fastdfe/annotation.py b/fastdfe/annotation.py
index 4861438f9..d86eda9ee 100644
--- a/fastdfe/annotation.py
+++ b/fastdfe/annotation.py
@@ -1860,7 +1860,10 @@ def _setup(self, handler: MultiHandler):
         })
 
         # set reader
-        self._reader = self._handler.load_vcf()
+        if self._handler.is_zarr_store:
+            self._reader = self._handler.load_zarr()
+        else:
+            self._reader = self._handler.load_vcf()
 
         # prepare masks
         self._prepare_masks(handler._reader.samples)
@@ -4452,7 +4455,8 @@ def _setup(self):
             annotation._setup(self)
 
         # create the writer
-        self._writer = Writer(self.output, self._reader)
+        if not self.is_zarr_store:
+            self._writer = Writer(self.output, self._reader)
 
     def _teardown(self):
         """
@@ -4462,8 +4466,9 @@ def _teardown(self):
             annotation._teardown()
 
         # close the writer and reader
-        self._writer.close()
-        self._reader.close()
+        if not self.is_zarr_store:
+            self._writer.close()
+            self._reader.close()
 
     def annotate(self):
         """
@@ -4485,7 +4490,8 @@ def annotate(self):
                     annotation.annotate_site(variant)
 
                 # write the variant
-                self._writer.write_record(variant)
+                if not self.is_zarr_store:
+                    self._writer.write_record(variant)
 
                 # update the progress bar
                 pbar.update()
diff --git a/fastdfe/io_handlers.py b/fastdfe/io_handlers.py
index 5ac73e5b0..e5614f1e1 100644
--- a/fastdfe/io_handlers.py
+++ b/fastdfe/io_handlers.py
@@ -27,6 +27,9 @@
 from pandas.errors import SettingWithCopyWarning
 from tqdm import tqdm
 
+import zarr
+from vcztools import retrieval
+
 from .settings import Settings
 
 #: The DNA bases
@@ -616,6 +619,8 @@ def __init__(
         #: Random generator instance
         self.rng = np.random.default_rng(seed=seed)
 
+        self.is_zarr_store = False
+
     @cached_property
     def _reader(self) -> 'cyvcf2.VCF':
         """
@@ -623,6 +628,9 @@ def _reader(self) -> 'cyvcf2.VCF':
 
         :return: The VCF reader.
         """
+        if os.path.isdir(self.vcf) and self.vcf.endswith('.vcz'):
+            self.is_zarr_store = True
+            return self.load_zarr()
         return self.load_vcf()
 
     def _rewind(self):
@@ -651,6 +659,18 @@ def load_vcf(self) -> 'cyvcf2.VCF':
 
         return VCF(self.download_if_url(self.vcf))
 
+
+    def load_zarr(self):
+        """
+        Load a Zarr file into a dictionary.
+
+        :return: The Zarr reader.
+        """
+        self._logger.info("Loading Zarr file")
+
+        return ZarrStore(self.vcf)
+
+
     @cached_property
     def n_sites(self) -> int:
         """
@@ -666,6 +686,9 @@ def count_sites(self) -> int:
 
         :return: Number of sites
         """
+        if self.is_zarr_store:
+            return self._reader.count_sites()
+
         return count_sites(
             vcf=self.download_if_url(self.vcf),
             max_sites=self.max_sites,
@@ -687,6 +710,81 @@ def get_pbar(self, desc: str = "Processing sites", total: int | None = 0) -> tqd
         )
 
 
+class ZarrVariant:
+    def __init__(
+        self,
+        ref: str,
+        chrom: str,
+        pos: int,
+        gt_bases: np.ndarray,
+    ):
+        self.REF = ref
+        self.CHROM = chrom
+        self.POS = pos
+        self.INFO = {}
+        self.gt_bases = gt_bases
+        self.is_snp = True
+
+
+class ZarrStore:
+
+    def __init__(self, fname: str, samples: List[str] = None):
+        """
+        Initialize a Zarr store.
+
+        The iterator iterates over Variant objects.
+
+        :param fname: The file name
+        """
+        self.fname = fname
+        self.root = zarr.open(fname, mode='r')
+        all_samples = self.root["sample_id"][:]
+        self.samples = list(retrieval.parse_samples(samples, all_samples)[0])
+        self.iter = retrieval.variant_iter(
+            fname,
+            samples=samples,
+            fields=["variant_contig", "variant_position", "variant_allele",
+                    "call_genotype", "call_genotype_phased"]
+        )
+
+    def __enter__(self):
+        return self
+
+    def __iter__(self):
+        return self
+
+    def __next__(self):
+        v = next(self.iter)
+        alleles = v["variant_allele"]
+        phased = v["call_genotype_phased"]
+        gt_bases = np.array([
+            ["/", "|"][np.int8(ph)].join(alleles[gt]) for ph, gt in zip(phased, v["call_genotype"])
+        ])
+        return ZarrVariant(
+            ref=alleles[0],
+            chrom=v["variant_contig"],
+            pos=v["variant_position"],
+            gt_bases=gt_bases,
+        )
+
+    def count_sites(self) -> int:
+        """
+        Count the number of sites in the Zarr store.
+
+        :return: Number of sites
+        """
+        return self.root["variant_id"].shape[0]
+
+    def add_info_to_header(self, header):
+        """
+        Add the info fields to the header.
+
+        :param header: The header
+        """
+        print("Adding info to header: ", header)
+        pass
+
+
 class MultiHandler(VCFHandler, FASTAHandler, GFFHandler):
     """
     Handle VCF, FASTA and GFF files.
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/.zattrs
new file mode 100644
index 000000000..39802e39a
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/.zattrs
@@ -0,0 +1,34 @@
+{
+    "source": "bio2zarr-0.1.6",
+    "vcf_meta_information": [
+        [
+            "fileformat",
+            "VCFv4.2"
+        ],
+        [
+            "ALT",
+            "<ID=NON_REF,Description=\"Represents any possible alternative allele not already represented at this location by REF and ALT\">"
+        ],
+        [
+            "GATKCommandLine",
+            "<ID=GenomicsDBImport,CommandLine=\"GenomicsDBImport --genomicsdb-workspace-path results/default/variants/genomics_dbs/db72 --variant results/default/variants/haplotypes/ASP01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP03/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP12/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP21/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP50/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP55/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP56/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA12/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR03/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR12/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR21/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR25a/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR25b/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR27a/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR27b/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU12/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU53/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU57/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU59/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU60/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU63/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU69/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU70/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU73/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU74/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU78/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU80/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU81/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU82/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU84/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU87/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK03/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK21/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK29/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA03/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA29/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK21/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK31/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU03/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU29/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU31/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU32/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU33/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN03/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN21/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN29/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN32/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN33/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN34/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK12/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK29/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK31/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK32/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK33/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK35/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK36/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK37/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK38/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK39/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK40/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK41/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK42/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK43/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED21/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED31/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR12/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR21/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR29/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR31/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR32/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT03/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT12/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT13D/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT29/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA34/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA35/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA39/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA40/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA42/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA43/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA44/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA45/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA46/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA49/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA51/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA55/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA57/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL51/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL52/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL53/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL54/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL55/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL57/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL58/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL64/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL68/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL71/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL72/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL74/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL75/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL77/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL78/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL82/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL83/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL92/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL93/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL94/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL97/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ERR2103730/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ERR2103731/all.sorted.g.vcf.gz --batch-size 10 --intervals results/default/variants/intervals/intervals72.bed --interval-padding 100 --tmp-dir /scratch/30147381 --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --overwrite-existing-genomicsdb-workspace false --consolidate false --validate-sample-name-map false --merge-input-intervals false --reader-threads 1 --max-num-intervals-to-import-in-parallel 1 --merge-contigs-into-num-partitions 0 --genomicsdb-shared-posixfs-optimizations false --genomicsdb-use-gcs-hdfs-connector false --interval-set-rule UNION --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 0 --cloud-index-prefetch-buffer 0 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false\",Version=\"4.2.2.0\",Date=\"October 2, 2022 9:27:30 AM CEST\">"
+        ],
+        [
+            "VEP",
+            "\"v104\" time=\"2022-10-02 10:23:11\" ensembl-funcgen=104.59ae779 ensembl=104.1af1dce ensembl-variation=104.6154f8b ensembl-io=104.1d3bb6e"
+        ],
+        [
+            "bcftools_viewCommand",
+            "view -Oz --apply-filters .,PASS --max-alleles 2 --exclude-types indels,mnps,other results/default/variants/vcfs/variants72.quality.tagged.vcf.gz"
+        ],
+        [
+            "bcftools_viewVersion",
+            "1.3.1+htslib-1.3.1"
+        ],
+        [
+            "source",
+            "GenomicsDBImport"
+        ]
+    ],
+    "vcf_zarr_version": "0.4"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/.zgroup b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/.zgroup
new file mode 100644
index 000000000..3b7daf227
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/.zgroup
@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/.zmetadata b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/.zmetadata
new file mode 100644
index 000000000..929b77906
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/.zmetadata
@@ -0,0 +1,1603 @@
+{
+    "metadata": {
+        ".zattrs": {
+            "source": "bio2zarr-0.1.6",
+            "vcf_meta_information": [
+                [
+                    "fileformat",
+                    "VCFv4.2"
+                ],
+                [
+                    "ALT",
+                    "<ID=NON_REF,Description=\"Represents any possible alternative allele not already represented at this location by REF and ALT\">"
+                ],
+                [
+                    "GATKCommandLine",
+                    "<ID=GenomicsDBImport,CommandLine=\"GenomicsDBImport --genomicsdb-workspace-path results/default/variants/genomics_dbs/db72 --variant results/default/variants/haplotypes/ASP01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP03/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP12/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP21/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP50/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP55/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ASP56/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA12/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BRA30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR03/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR12/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR21/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR25a/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR25b/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR27a/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/BUR27b/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU12/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU53/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU57/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU59/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU60/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU63/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU69/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU70/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU73/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU74/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU78/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU80/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU81/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU82/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU84/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DJU87/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK03/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK21/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK29/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/DOK30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA03/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA29/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/GNA30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK21/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/JOKK31/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU03/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU29/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU31/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU32/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/KAU33/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN03/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN21/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN29/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN32/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN33/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/LIN34/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK12/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK29/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK31/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK32/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK33/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK35/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK36/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK37/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK38/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK39/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK40/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK41/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK42/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/MOK43/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED21/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NED31/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR12/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR15/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR21/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR27/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR29/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR31/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/NOR32/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT01/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT03/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT09/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT11/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT12/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT13D/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT14/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT16/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT17/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT18/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT25/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT26/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT29/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/PIT30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA02/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA08/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA10/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA13/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA19/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA20/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA22/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA23/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA24/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA28/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA30/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA34/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA35/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA39/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA40/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA42/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA43/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA44/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA45/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA46/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA49/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA51/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA55/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/SKA57/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL04/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL05/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL06/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL07/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL51/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL52/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL53/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL54/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL55/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL57/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL58/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL64/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL68/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL71/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL72/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL74/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL75/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL77/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL78/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL82/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL83/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL92/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL93/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL94/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/VAL97/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ERR2103730/all.sorted.g.vcf.gz --variant results/default/variants/haplotypes/ERR2103731/all.sorted.g.vcf.gz --batch-size 10 --intervals results/default/variants/intervals/intervals72.bed --interval-padding 100 --tmp-dir /scratch/30147381 --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --overwrite-existing-genomicsdb-workspace false --consolidate false --validate-sample-name-map false --merge-input-intervals false --reader-threads 1 --max-num-intervals-to-import-in-parallel 1 --merge-contigs-into-num-partitions 0 --genomicsdb-shared-posixfs-optimizations false --genomicsdb-use-gcs-hdfs-connector false --interval-set-rule UNION --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 0 --cloud-index-prefetch-buffer 0 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false\",Version=\"4.2.2.0\",Date=\"October 2, 2022 9:27:30 AM CEST\">"
+                ],
+                [
+                    "VEP",
+                    "\"v104\" time=\"2022-10-02 10:23:11\" ensembl-funcgen=104.59ae779 ensembl=104.1af1dce ensembl-variation=104.6154f8b ensembl-io=104.1d3bb6e"
+                ],
+                [
+                    "bcftools_viewCommand",
+                    "view -Oz --apply-filters .,PASS --max-alleles 2 --exclude-types indels,mnps,other results/default/variants/vcfs/variants72.quality.tagged.vcf.gz"
+                ],
+                [
+                    "bcftools_viewVersion",
+                    "1.3.1+htslib-1.3.1"
+                ],
+                [
+                    "source",
+                    "GenomicsDBImport"
+                ]
+            ],
+            "vcf_zarr_version": "0.4"
+        },
+        ".zgroup": {
+            "zarr_format": 2
+        },
+        "call_AD/.zarray": {
+            "chunks": [
+                1000,
+                379,
+                2
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<i2",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                379,
+                2
+            ],
+            "zarr_format": 2
+        },
+        "call_AD/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "samples",
+                "alleles"
+            ],
+            "description": "Allelic depths for the ref and alt alleles in the order listed"
+        },
+        "call_DP/.zarray": {
+            "chunks": [
+                1000,
+                379
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<i2",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                379
+            ],
+            "zarr_format": 2
+        },
+        "call_DP/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "samples"
+            ],
+            "description": "Approximate read depth (reads with MQ=255 or with bad mates are filtered)"
+        },
+        "call_GQ/.zarray": {
+            "chunks": [
+                1000,
+                379
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|i1",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                379
+            ],
+            "zarr_format": 2
+        },
+        "call_GQ/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "samples"
+            ],
+            "description": "Genotype Quality"
+        },
+        "call_MIN_DP/.zarray": {
+            "chunks": [
+                1000,
+                379
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|i1",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                379
+            ],
+            "zarr_format": 2
+        },
+        "call_MIN_DP/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "samples"
+            ],
+            "description": "Minimum DP observed within the GVCF block"
+        },
+        "call_PGT/.zarray": {
+            "chunks": [
+                1000,
+                379
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|O",
+            "fill_value": null,
+            "filters": [
+                {
+                    "id": "vlen-utf8"
+                }
+            ],
+            "order": "C",
+            "shape": [
+                10000,
+                379
+            ],
+            "zarr_format": 2
+        },
+        "call_PGT/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "samples"
+            ],
+            "description": "Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles"
+        },
+        "call_PID/.zarray": {
+            "chunks": [
+                1000,
+                379
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|O",
+            "fill_value": null,
+            "filters": [
+                {
+                    "id": "vlen-utf8"
+                }
+            ],
+            "order": "C",
+            "shape": [
+                10000,
+                379
+            ],
+            "zarr_format": 2
+        },
+        "call_PID/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "samples"
+            ],
+            "description": "Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"
+        },
+        "call_PL/.zarray": {
+            "chunks": [
+                1000,
+                379,
+                3
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<i4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                379,
+                3
+            ],
+            "zarr_format": 2
+        },
+        "call_PL/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "samples",
+                "genotypes"
+            ],
+            "description": "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"
+        },
+        "call_PS/.zarray": {
+            "chunks": [
+                1000,
+                379
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<i4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                379
+            ],
+            "zarr_format": 2
+        },
+        "call_PS/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "samples"
+            ],
+            "description": "Phasing set (typically the position of the first variant in the set)"
+        },
+        "call_RGQ/.zarray": {
+            "chunks": [
+                1000,
+                379
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|i1",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                379
+            ],
+            "zarr_format": 2
+        },
+        "call_RGQ/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "samples"
+            ],
+            "description": "Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)"
+        },
+        "call_SB/.zarray": {
+            "chunks": [
+                1000,
+                379,
+                4
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|i1",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                379,
+                4
+            ],
+            "zarr_format": 2
+        },
+        "call_SB/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "samples",
+                "FORMAT_SB_dim"
+            ],
+            "description": "Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."
+        },
+        "call_genotype/.zarray": {
+            "chunks": [
+                1000,
+                379,
+                2
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 2
+            },
+            "dimension_separator": "/",
+            "dtype": "|i1",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                379,
+                2
+            ],
+            "zarr_format": 2
+        },
+        "call_genotype/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "samples",
+                "ploidy"
+            ],
+            "description": ""
+        },
+        "call_genotype_mask/.zarray": {
+            "chunks": [
+                1000,
+                379,
+                2
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 2
+            },
+            "dimension_separator": "/",
+            "dtype": "|b1",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                379,
+                2
+            ],
+            "zarr_format": 2
+        },
+        "call_genotype_mask/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "samples",
+                "ploidy"
+            ],
+            "description": ""
+        },
+        "call_genotype_phased/.zarray": {
+            "chunks": [
+                1000,
+                379
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 2
+            },
+            "dimension_separator": "/",
+            "dtype": "|b1",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                379
+            ],
+            "zarr_format": 2
+        },
+        "call_genotype_phased/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "samples"
+            ],
+            "description": ""
+        },
+        "contig_id/.zarray": {
+            "chunks": [
+                5642
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dtype": "|O",
+            "fill_value": 0,
+            "filters": [
+                {
+                    "id": "vlen-utf8"
+                }
+            ],
+            "order": "C",
+            "shape": [
+                5642
+            ],
+            "zarr_format": 2
+        },
+        "contig_id/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "contigs"
+            ]
+        },
+        "contig_length/.zarray": {
+            "chunks": [
+                5642
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dtype": "<i8",
+            "fill_value": 0,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                5642
+            ],
+            "zarr_format": 2
+        },
+        "contig_length/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "contigs"
+            ]
+        },
+        "filter_description/.zarray": {
+            "chunks": [
+                7
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dtype": "|O",
+            "fill_value": 0,
+            "filters": [
+                {
+                    "id": "vlen-utf8"
+                }
+            ],
+            "order": "C",
+            "shape": [
+                7
+            ],
+            "zarr_format": 2
+        },
+        "filter_description/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "filters"
+            ]
+        },
+        "filter_id/.zarray": {
+            "chunks": [
+                7
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dtype": "|O",
+            "fill_value": 0,
+            "filters": [
+                {
+                    "id": "vlen-utf8"
+                }
+            ],
+            "order": "C",
+            "shape": [
+                7
+            ],
+            "zarr_format": 2
+        },
+        "filter_id/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "filters"
+            ]
+        },
+        "region_index/.zarray": {
+            "chunks": [
+                12,
+                6
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 9,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 0
+            },
+            "dimension_separator": "/",
+            "dtype": "<i4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                12,
+                6
+            ],
+            "zarr_format": 2
+        },
+        "region_index/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "region_index_values",
+                "region_index_fields"
+            ]
+        },
+        "sample_id/.zarray": {
+            "chunks": [
+                379
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dtype": "|O",
+            "fill_value": 0,
+            "filters": [
+                {
+                    "id": "vlen-utf8"
+                }
+            ],
+            "order": "C",
+            "shape": [
+                379
+            ],
+            "zarr_format": 2
+        },
+        "sample_id/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "samples"
+            ]
+        },
+        "variant_AA/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|O",
+            "fill_value": null,
+            "filters": [
+                {
+                    "id": "vlen-utf8"
+                }
+            ],
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_AA/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Ancestral Allele"
+        },
+        "variant_AC/.zarray": {
+            "chunks": [
+                1000,
+                1
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<i2",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                1
+            ],
+            "zarr_format": 2
+        },
+        "variant_AC/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "alt_alleles"
+            ],
+            "description": "Allele count in genotypes, for each ALT allele, in the same order as listed"
+        },
+        "variant_AF/.zarray": {
+            "chunks": [
+                1000,
+                1
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<f4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                1
+            ],
+            "zarr_format": 2
+        },
+        "variant_AF/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "alt_alleles"
+            ],
+            "description": "Allele Frequency, for each ALT allele, in the same order as listed"
+        },
+        "variant_AN/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<i2",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_AN/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Total number of alleles in called genotypes"
+        },
+        "variant_BaseQRankSum/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<f4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_BaseQRankSum/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"
+        },
+        "variant_CSQ/.zarray": {
+            "chunks": [
+                1000,
+                3
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|O",
+            "fill_value": null,
+            "filters": [
+                {
+                    "id": "vlen-utf8"
+                }
+            ],
+            "order": "C",
+            "shape": [
+                10000,
+                3
+            ],
+            "zarr_format": 2
+        },
+        "variant_CSQ/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "INFO_CSQ_dim"
+            ],
+            "description": "Consequence annotations from Ensembl VEP. Format: Consequence|Codons"
+        },
+        "variant_DP/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<i4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_DP/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Approximate read depth; some reads may have been filtered"
+        },
+        "variant_Degeneracy/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|i1",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_Degeneracy/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "n-fold degeneracy"
+        },
+        "variant_Degeneracy_Info/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|O",
+            "fill_value": null,
+            "filters": [
+                {
+                    "id": "vlen-utf8"
+                }
+            ],
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_Degeneracy_Info/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Additional information about custom degeneracy annotation:"
+        },
+        "variant_END/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|i1",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_END/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Stop position of the interval"
+        },
+        "variant_EST_SFS_input/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|O",
+            "fill_value": null,
+            "filters": [
+                {
+                    "id": "vlen-utf8"
+                }
+            ],
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_EST_SFS_input/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "EST-SFS input"
+        },
+        "variant_EST_SFS_probs/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|O",
+            "fill_value": null,
+            "filters": [
+                {
+                    "id": "vlen-utf8"
+                }
+            ],
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_EST_SFS_probs/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "EST-SFS probabilities"
+        },
+        "variant_ExcessHet/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<f4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_ExcessHet/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Phred-scaled p-value for exact test of excess heterozygosity"
+        },
+        "variant_FS/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<f4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_FS/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Phred-scaled p-value using Fisher's exact test to detect strand bias"
+        },
+        "variant_InbreedingCoeff/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<f4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_InbreedingCoeff/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"
+        },
+        "variant_MLEAC/.zarray": {
+            "chunks": [
+                1000,
+                1
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<i2",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                1
+            ],
+            "zarr_format": 2
+        },
+        "variant_MLEAC/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "alt_alleles"
+            ],
+            "description": "Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"
+        },
+        "variant_MLEAF/.zarray": {
+            "chunks": [
+                1000,
+                1
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<f4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                1
+            ],
+            "zarr_format": 2
+        },
+        "variant_MLEAF/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "alt_alleles"
+            ],
+            "description": "Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"
+        },
+        "variant_MQ/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<f4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_MQ/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "RMS Mapping Quality"
+        },
+        "variant_MQRankSum/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<f4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_MQRankSum/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"
+        },
+        "variant_QD/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<f4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_QD/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Variant Confidence/Quality by Depth"
+        },
+        "variant_RAW_MQandDP/.zarray": {
+            "chunks": [
+                1000,
+                2
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|i1",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                2
+            ],
+            "zarr_format": 2
+        },
+        "variant_RAW_MQandDP/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "INFO_RAW_MQandDP_dim"
+            ],
+            "description": "Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation."
+        },
+        "variant_ReadPosRankSum/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<f4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_ReadPosRankSum/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"
+        },
+        "variant_SOR/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<f4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_SOR/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"
+        },
+        "variant_Synonymy/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|i1",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_Synonymy/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Whether coding site is synonymous"
+        },
+        "variant_Synonymy_Info/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|O",
+            "fill_value": null,
+            "filters": [
+                {
+                    "id": "vlen-utf8"
+                }
+            ],
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_Synonymy_Info/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Additional information about custom synonymy annotation:"
+        },
+        "variant_allele/.zarray": {
+            "chunks": [
+                1000,
+                2
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|O",
+            "fill_value": null,
+            "filters": [
+                {
+                    "id": "vlen-utf8"
+                }
+            ],
+            "order": "C",
+            "shape": [
+                10000,
+                2
+            ],
+            "zarr_format": 2
+        },
+        "variant_allele/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "alleles"
+            ],
+            "description": "List of the reference and alternate alleles"
+        },
+        "variant_contig/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<i2",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_contig/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file"
+        },
+        "variant_filter/.zarray": {
+            "chunks": [
+                1000,
+                7
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 2
+            },
+            "dimension_separator": "/",
+            "dtype": "|b1",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000,
+                7
+            ],
+            "zarr_format": 2
+        },
+        "variant_filter/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants",
+                "filters"
+            ],
+            "description": "Filter status of the variant"
+        },
+        "variant_genome.corrected.gff.gz/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|O",
+            "fill_value": null,
+            "filters": [
+                {
+                    "id": "vlen-utf8"
+                }
+            ],
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_genome.corrected.gff.gz/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "resources/reference/genome.corrected.gff.gz (overlap)"
+        },
+        "variant_id/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|O",
+            "fill_value": null,
+            "filters": [
+                {
+                    "id": "vlen-utf8"
+                }
+            ],
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_id/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "List of unique identifiers where applicable"
+        },
+        "variant_id_mask/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 2
+            },
+            "dimension_separator": "/",
+            "dtype": "|b1",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_id_mask/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": ""
+        },
+        "variant_length/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "|i1",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_length/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "The length of the variant measured in bases"
+        },
+        "variant_position/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<i4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_position/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "The reference position"
+        },
+        "variant_quality/.zarray": {
+            "chunks": [
+                1000
+            ],
+            "compressor": {
+                "blocksize": 0,
+                "clevel": 7,
+                "cname": "zstd",
+                "id": "blosc",
+                "shuffle": 1
+            },
+            "dimension_separator": "/",
+            "dtype": "<f4",
+            "fill_value": null,
+            "filters": null,
+            "order": "C",
+            "shape": [
+                10000
+            ],
+            "zarr_format": 2
+        },
+        "variant_quality/.zattrs": {
+            "_ARRAY_DIMENSIONS": [
+                "variants"
+            ],
+            "description": "Phred-scaled quality score"
+        }
+    },
+    "zarr_consolidated_format": 1
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/.zarray
new file mode 100644
index 000000000..38490603d
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/.zarray
@@ -0,0 +1,25 @@
+{
+    "chunks": [
+        1000,
+        379,
+        2
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<i2",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        379,
+        2
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/.zattrs
new file mode 100644
index 000000000..b7b9dae2d
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/.zattrs
@@ -0,0 +1,8 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "samples",
+        "alleles"
+    ],
+    "description": "Allelic depths for the ref and alt alleles in the order listed"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/0/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/0/0/0
new file mode 100644
index 000000000..15081b020
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/0/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/1/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/1/0/0
new file mode 100644
index 000000000..0b6f234eb
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/1/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/2/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/2/0/0
new file mode 100644
index 000000000..8f2f6f863
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/2/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/3/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/3/0/0
new file mode 100644
index 000000000..c81b830d3
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/3/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/4/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/4/0/0
new file mode 100644
index 000000000..05175ac63
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/4/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/5/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/5/0/0
new file mode 100644
index 000000000..f8145fe18
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/5/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/6/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/6/0/0
new file mode 100644
index 000000000..f3d1cec0b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/6/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/7/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/7/0/0
new file mode 100644
index 000000000..7ddd0fc2a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/7/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/8/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/8/0/0
new file mode 100644
index 000000000..c57d598ac
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/8/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/9/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/9/0/0
new file mode 100644
index 000000000..a37db6fd7
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_AD/9/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/.zarray
new file mode 100644
index 000000000..52d4d6688
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/.zarray
@@ -0,0 +1,23 @@
+{
+    "chunks": [
+        1000,
+        379
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<i2",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        379
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/.zattrs
new file mode 100644
index 000000000..e8c0a8cef
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "samples"
+    ],
+    "description": "Approximate read depth (reads with MQ=255 or with bad mates are filtered)"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/0/0
new file mode 100644
index 000000000..fde4bc0c6
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/1/0
new file mode 100644
index 000000000..047d771e6
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/2/0
new file mode 100644
index 000000000..5dba6f1d4
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/3/0
new file mode 100644
index 000000000..dde9a4376
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/4/0
new file mode 100644
index 000000000..ff9421079
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/5/0
new file mode 100644
index 000000000..03d7c2e89
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/6/0
new file mode 100644
index 000000000..5bfb3b8b5
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/7/0
new file mode 100644
index 000000000..1a3257d63
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/8/0
new file mode 100644
index 000000000..f98016320
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/9/0
new file mode 100644
index 000000000..1394db80d
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_DP/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/.zarray
new file mode 100644
index 000000000..562b78e86
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/.zarray
@@ -0,0 +1,23 @@
+{
+    "chunks": [
+        1000,
+        379
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|i1",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        379
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/.zattrs
new file mode 100644
index 000000000..11c6e37d4
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "samples"
+    ],
+    "description": "Genotype Quality"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/0/0
new file mode 100644
index 000000000..5047810c4
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/1/0
new file mode 100644
index 000000000..ed14e6d17
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/2/0
new file mode 100644
index 000000000..67be98dfe
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/3/0
new file mode 100644
index 000000000..6094b04c1
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/4/0
new file mode 100644
index 000000000..ed4566051
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/5/0
new file mode 100644
index 000000000..b2c27e4d3
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/6/0
new file mode 100644
index 000000000..6bf0690cc
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/7/0
new file mode 100644
index 000000000..c6404ab50
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/8/0
new file mode 100644
index 000000000..24aa23f16
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/9/0
new file mode 100644
index 000000000..26526e837
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_GQ/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/.zarray
new file mode 100644
index 000000000..562b78e86
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/.zarray
@@ -0,0 +1,23 @@
+{
+    "chunks": [
+        1000,
+        379
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|i1",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        379
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/.zattrs
new file mode 100644
index 000000000..11c781594
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "samples"
+    ],
+    "description": "Minimum DP observed within the GVCF block"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/0/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/1/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/2/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/3/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/4/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/5/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/6/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/7/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/8/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/9/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_MIN_DP/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/.zarray
new file mode 100644
index 000000000..9774064eb
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/.zarray
@@ -0,0 +1,27 @@
+{
+    "chunks": [
+        1000,
+        379
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|O",
+    "fill_value": null,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        10000,
+        379
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/.zattrs
new file mode 100644
index 000000000..bb1c12064
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "samples"
+    ],
+    "description": "Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/0/0
new file mode 100644
index 000000000..68ce3d464
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/1/0
new file mode 100644
index 000000000..227c6dc9a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/2/0
new file mode 100644
index 000000000..405810811
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/3/0
new file mode 100644
index 000000000..22b3806b4
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/4/0
new file mode 100644
index 000000000..e80bc1b67
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/5/0
new file mode 100644
index 000000000..64ed003ae
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/6/0
new file mode 100644
index 000000000..7ab20de6d
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/7/0
new file mode 100644
index 000000000..141989575
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/8/0
new file mode 100644
index 000000000..e0be549f6
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/9/0
new file mode 100644
index 000000000..2fa5af9b5
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PGT/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/.zarray
new file mode 100644
index 000000000..9774064eb
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/.zarray
@@ -0,0 +1,27 @@
+{
+    "chunks": [
+        1000,
+        379
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|O",
+    "fill_value": null,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        10000,
+        379
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/.zattrs
new file mode 100644
index 000000000..5d34aaac6
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "samples"
+    ],
+    "description": "Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/0/0
new file mode 100644
index 000000000..6c25f169e
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/1/0
new file mode 100644
index 000000000..966071427
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/2/0
new file mode 100644
index 000000000..1c4936d76
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/3/0
new file mode 100644
index 000000000..bc9a72eb3
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/4/0
new file mode 100644
index 000000000..d573e3345
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/5/0
new file mode 100644
index 000000000..57f4e65a4
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/6/0
new file mode 100644
index 000000000..f8e09a556
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/7/0
new file mode 100644
index 000000000..99524bb0a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/8/0
new file mode 100644
index 000000000..e34210752
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/9/0
new file mode 100644
index 000000000..d87d1cb0d
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PID/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/.zarray
new file mode 100644
index 000000000..5f480cfbd
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/.zarray
@@ -0,0 +1,25 @@
+{
+    "chunks": [
+        1000,
+        379,
+        3
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<i4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        379,
+        3
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/.zattrs
new file mode 100644
index 000000000..e4bb40e8d
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/.zattrs
@@ -0,0 +1,8 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "samples",
+        "genotypes"
+    ],
+    "description": "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/0/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/0/0/0
new file mode 100644
index 000000000..fccd18b0e
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/0/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/1/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/1/0/0
new file mode 100644
index 000000000..159b04788
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/1/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/2/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/2/0/0
new file mode 100644
index 000000000..b0844ca8e
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/2/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/3/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/3/0/0
new file mode 100644
index 000000000..4e5b766f5
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/3/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/4/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/4/0/0
new file mode 100644
index 000000000..82e32e287
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/4/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/5/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/5/0/0
new file mode 100644
index 000000000..0c1232729
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/5/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/6/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/6/0/0
new file mode 100644
index 000000000..ab7618e2d
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/6/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/7/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/7/0/0
new file mode 100644
index 000000000..417b89f9f
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/7/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/8/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/8/0/0
new file mode 100644
index 000000000..a05258d50
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/8/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/9/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/9/0/0
new file mode 100644
index 000000000..da772cb32
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PL/9/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/.zarray
new file mode 100644
index 000000000..71b87fffa
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/.zarray
@@ -0,0 +1,23 @@
+{
+    "chunks": [
+        1000,
+        379
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<i4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        379
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/.zattrs
new file mode 100644
index 000000000..97f9ea922
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "samples"
+    ],
+    "description": "Phasing set (typically the position of the first variant in the set)"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/0/0
new file mode 100644
index 000000000..84871480d
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/1/0
new file mode 100644
index 000000000..fb91d9fce
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/2/0
new file mode 100644
index 000000000..8c57dc819
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/3/0
new file mode 100644
index 000000000..e1d32d26d
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/4/0
new file mode 100644
index 000000000..a0e4a7d2a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/5/0
new file mode 100644
index 000000000..402bd0f6f
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/6/0
new file mode 100644
index 000000000..aab8b9b17
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/7/0
new file mode 100644
index 000000000..6dd76c357
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/8/0
new file mode 100644
index 000000000..512dccef3
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/9/0
new file mode 100644
index 000000000..501d1ff67
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_PS/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/.zarray
new file mode 100644
index 000000000..562b78e86
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/.zarray
@@ -0,0 +1,23 @@
+{
+    "chunks": [
+        1000,
+        379
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|i1",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        379
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/.zattrs
new file mode 100644
index 000000000..5abb10fce
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "samples"
+    ],
+    "description": "Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/0/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/1/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/2/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/3/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/4/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/5/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/6/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/7/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/8/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/9/0
new file mode 100644
index 000000000..542a787b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_RGQ/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/.zarray
new file mode 100644
index 000000000..aac2fa1f8
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/.zarray
@@ -0,0 +1,25 @@
+{
+    "chunks": [
+        1000,
+        379,
+        4
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|i1",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        379,
+        4
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/.zattrs
new file mode 100644
index 000000000..57eae68a5
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/.zattrs
@@ -0,0 +1,8 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "samples",
+        "FORMAT_SB_dim"
+    ],
+    "description": "Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/0/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/0/0/0
new file mode 100644
index 000000000..84219917b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/0/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/1/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/1/0/0
new file mode 100644
index 000000000..84219917b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/1/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/2/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/2/0/0
new file mode 100644
index 000000000..84219917b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/2/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/3/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/3/0/0
new file mode 100644
index 000000000..84219917b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/3/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/4/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/4/0/0
new file mode 100644
index 000000000..84219917b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/4/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/5/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/5/0/0
new file mode 100644
index 000000000..84219917b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/5/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/6/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/6/0/0
new file mode 100644
index 000000000..84219917b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/6/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/7/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/7/0/0
new file mode 100644
index 000000000..84219917b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/7/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/8/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/8/0/0
new file mode 100644
index 000000000..84219917b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/8/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/9/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/9/0/0
new file mode 100644
index 000000000..84219917b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_SB/9/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/.zarray
new file mode 100644
index 000000000..54500c929
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/.zarray
@@ -0,0 +1,25 @@
+{
+    "chunks": [
+        1000,
+        379,
+        2
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 2
+    },
+    "dimension_separator": "/",
+    "dtype": "|i1",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        379,
+        2
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/.zattrs
new file mode 100644
index 000000000..61388a628
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/.zattrs
@@ -0,0 +1,8 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "samples",
+        "ploidy"
+    ],
+    "description": ""
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/0/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/0/0/0
new file mode 100644
index 000000000..ced51bf8b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/0/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/1/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/1/0/0
new file mode 100644
index 000000000..9359ce108
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/1/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/2/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/2/0/0
new file mode 100644
index 000000000..df04e4208
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/2/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/3/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/3/0/0
new file mode 100644
index 000000000..589f64c6a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/3/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/4/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/4/0/0
new file mode 100644
index 000000000..d175646c4
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/4/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/5/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/5/0/0
new file mode 100644
index 000000000..f03d2f31b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/5/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/6/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/6/0/0
new file mode 100644
index 000000000..5bfe6cce0
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/6/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/7/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/7/0/0
new file mode 100644
index 000000000..b7d2da2d1
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/7/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/8/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/8/0/0
new file mode 100644
index 000000000..2b5135b2e
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/8/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/9/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/9/0/0
new file mode 100644
index 000000000..61b1a07c8
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype/9/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/.zarray
new file mode 100644
index 000000000..5de2edf61
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/.zarray
@@ -0,0 +1,25 @@
+{
+    "chunks": [
+        1000,
+        379,
+        2
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 2
+    },
+    "dimension_separator": "/",
+    "dtype": "|b1",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        379,
+        2
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/.zattrs
new file mode 100644
index 000000000..61388a628
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/.zattrs
@@ -0,0 +1,8 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "samples",
+        "ploidy"
+    ],
+    "description": ""
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/0/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/0/0/0
new file mode 100644
index 000000000..dc00cbece
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/0/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/1/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/1/0/0
new file mode 100644
index 000000000..aed360e8d
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/1/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/2/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/2/0/0
new file mode 100644
index 000000000..96aa5d774
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/2/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/3/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/3/0/0
new file mode 100644
index 000000000..9ab960e1d
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/3/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/4/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/4/0/0
new file mode 100644
index 000000000..56b7e3845
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/4/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/5/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/5/0/0
new file mode 100644
index 000000000..a528d8064
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/5/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/6/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/6/0/0
new file mode 100644
index 000000000..457ca449a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/6/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/7/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/7/0/0
new file mode 100644
index 000000000..81fb22135
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/7/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/8/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/8/0/0
new file mode 100644
index 000000000..13037a118
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/8/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/9/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/9/0/0
new file mode 100644
index 000000000..a24cb1fbd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_mask/9/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/.zarray
new file mode 100644
index 000000000..7fa300270
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/.zarray
@@ -0,0 +1,23 @@
+{
+    "chunks": [
+        1000,
+        379
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 2
+    },
+    "dimension_separator": "/",
+    "dtype": "|b1",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        379
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/.zattrs
new file mode 100644
index 000000000..a73d47739
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "samples"
+    ],
+    "description": ""
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/0/0
new file mode 100644
index 000000000..d98772fa1
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/1/0
new file mode 100644
index 000000000..88b441b97
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/2/0
new file mode 100644
index 000000000..e227dd0f0
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/3/0
new file mode 100644
index 000000000..ad294bcd5
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/4/0
new file mode 100644
index 000000000..acc4ff581
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/5/0
new file mode 100644
index 000000000..44411baaa
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/6/0
new file mode 100644
index 000000000..f8990bdfb
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/7/0
new file mode 100644
index 000000000..593813bd6
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/8/0
new file mode 100644
index 000000000..36d86fe80
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/9/0
new file mode 100644
index 000000000..8da5353be
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/call_genotype_phased/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_id/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_id/.zarray
new file mode 100644
index 000000000..aa6908d5b
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_id/.zarray
@@ -0,0 +1,24 @@
+{
+    "chunks": [
+        5642
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "|O",
+    "fill_value": 0,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        5642
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_id/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_id/.zattrs
new file mode 100644
index 000000000..74be636ba
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_id/.zattrs
@@ -0,0 +1,5 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "contigs"
+    ]
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_id/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_id/0
new file mode 100644
index 000000000..285aaa31e
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_id/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_length/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_length/.zarray
new file mode 100644
index 000000000..b04e2d673
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_length/.zarray
@@ -0,0 +1,20 @@
+{
+    "chunks": [
+        5642
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i8",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        5642
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_length/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_length/.zattrs
new file mode 100644
index 000000000..74be636ba
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_length/.zattrs
@@ -0,0 +1,5 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "contigs"
+    ]
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_length/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_length/0
new file mode 100644
index 000000000..c531a2944
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/contig_length/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_description/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_description/.zarray
new file mode 100644
index 000000000..a70bdbcfc
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_description/.zarray
@@ -0,0 +1,24 @@
+{
+    "chunks": [
+        7
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "|O",
+    "fill_value": 0,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        7
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_description/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_description/.zattrs
new file mode 100644
index 000000000..29d3e1568
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_description/.zattrs
@@ -0,0 +1,5 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "filters"
+    ]
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_description/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_description/0
new file mode 100644
index 000000000..54e174049
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_description/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_id/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_id/.zarray
new file mode 100644
index 000000000..a70bdbcfc
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_id/.zarray
@@ -0,0 +1,24 @@
+{
+    "chunks": [
+        7
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "|O",
+    "fill_value": 0,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        7
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_id/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_id/.zattrs
new file mode 100644
index 000000000..29d3e1568
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_id/.zattrs
@@ -0,0 +1,5 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "filters"
+    ]
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_id/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_id/0
new file mode 100644
index 000000000..6f70d6aa2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/filter_id/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/region_index/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/region_index/.zarray
new file mode 100644
index 000000000..a3bee83fb
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/region_index/.zarray
@@ -0,0 +1,23 @@
+{
+    "chunks": [
+        12,
+        6
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 9,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 0
+    },
+    "dimension_separator": "/",
+    "dtype": "<i4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        12,
+        6
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/region_index/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/region_index/.zattrs
new file mode 100644
index 000000000..545dd8f61
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/region_index/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "region_index_values",
+        "region_index_fields"
+    ]
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/region_index/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/region_index/0/0
new file mode 100644
index 000000000..f004e143f
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/region_index/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/sample_id/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/sample_id/.zarray
new file mode 100644
index 000000000..d9a939512
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/sample_id/.zarray
@@ -0,0 +1,24 @@
+{
+    "chunks": [
+        379
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "|O",
+    "fill_value": 0,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        379
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/sample_id/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/sample_id/.zattrs
new file mode 100644
index 000000000..4099b0324
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/sample_id/.zattrs
@@ -0,0 +1,5 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "samples"
+    ]
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/sample_id/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/sample_id/0
new file mode 100644
index 000000000..e08acae51
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/sample_id/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/.zarray
new file mode 100644
index 000000000..eb78fd611
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/.zarray
@@ -0,0 +1,25 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|O",
+    "fill_value": null,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/.zattrs
new file mode 100644
index 000000000..d9dba8b97
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Ancestral Allele"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/0
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/1
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/2
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/3
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/4
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/5
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/6
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/7
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/8
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/9
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AA/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/.zarray
new file mode 100644
index 000000000..56df8e061
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/.zarray
@@ -0,0 +1,23 @@
+{
+    "chunks": [
+        1000,
+        1
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<i2",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        1
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/.zattrs
new file mode 100644
index 000000000..127c70dd1
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "alt_alleles"
+    ],
+    "description": "Allele count in genotypes, for each ALT allele, in the same order as listed"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/0/0
new file mode 100644
index 000000000..9dc7700df
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/1/0
new file mode 100644
index 000000000..621acc9cd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/2/0
new file mode 100644
index 000000000..6ea465b0a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/3/0
new file mode 100644
index 000000000..2c1c5f0ba
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/4/0
new file mode 100644
index 000000000..102ed1ab8
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/5/0
new file mode 100644
index 000000000..66c009c79
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/6/0
new file mode 100644
index 000000000..d9fbbdf2f
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/7/0
new file mode 100644
index 000000000..ba5a74ddc
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/8/0
new file mode 100644
index 000000000..eb13252fd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/9/0
new file mode 100644
index 000000000..3060d6271
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AC/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/.zarray
new file mode 100644
index 000000000..2d0713a90
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/.zarray
@@ -0,0 +1,23 @@
+{
+    "chunks": [
+        1000,
+        1
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<f4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        1
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/.zattrs
new file mode 100644
index 000000000..897598438
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "alt_alleles"
+    ],
+    "description": "Allele Frequency, for each ALT allele, in the same order as listed"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/0/0
new file mode 100644
index 000000000..14ab3f083
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/1/0
new file mode 100644
index 000000000..6b6c8ca61
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/2/0
new file mode 100644
index 000000000..26f299b0d
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/3/0
new file mode 100644
index 000000000..10f202a39
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/4/0
new file mode 100644
index 000000000..0883784ca
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/5/0
new file mode 100644
index 000000000..3e75ad681
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/6/0
new file mode 100644
index 000000000..86573fbe9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/7/0
new file mode 100644
index 000000000..b5f60c5f4
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/8/0
new file mode 100644
index 000000000..d08f0493c
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/9/0
new file mode 100644
index 000000000..5d8c86c94
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AF/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/.zarray
new file mode 100644
index 000000000..8d42cfc5e
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<i2",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/.zattrs
new file mode 100644
index 000000000..548c8cf46
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Total number of alleles in called genotypes"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/0
new file mode 100644
index 000000000..76fa63550
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/1
new file mode 100644
index 000000000..2a338070f
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/2
new file mode 100644
index 000000000..d8b9ae908
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/3
new file mode 100644
index 000000000..f9bf64f86
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/4
new file mode 100644
index 000000000..b54824697
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/5
new file mode 100644
index 000000000..cb2c1a1f5
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/6
new file mode 100644
index 000000000..2b9ad7386
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/7
new file mode 100644
index 000000000..b35db752f
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/8
new file mode 100644
index 000000000..032b61252
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/9
new file mode 100644
index 000000000..e7fd6239d
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_AN/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/.zarray
new file mode 100644
index 000000000..618055d22
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<f4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/.zattrs
new file mode 100644
index 000000000..f55cd5d3d
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/0
new file mode 100644
index 000000000..610676ff6
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/1
new file mode 100644
index 000000000..8b08fce76
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/2
new file mode 100644
index 000000000..abb1e15e5
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/3
new file mode 100644
index 000000000..dab54be4c
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/4
new file mode 100644
index 000000000..697028a98
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/5
new file mode 100644
index 000000000..8401af958
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/6
new file mode 100644
index 000000000..b30ef1ff4
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/7
new file mode 100644
index 000000000..78688c65e
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/8
new file mode 100644
index 000000000..1f27b7fe1
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/9
new file mode 100644
index 000000000..850e8d2d4
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_BaseQRankSum/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/.zarray
new file mode 100644
index 000000000..f7a38063d
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/.zarray
@@ -0,0 +1,27 @@
+{
+    "chunks": [
+        1000,
+        3
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|O",
+    "fill_value": null,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        10000,
+        3
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/.zattrs
new file mode 100644
index 000000000..b35ec1497
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "INFO_CSQ_dim"
+    ],
+    "description": "Consequence annotations from Ensembl VEP. Format: Consequence|Codons"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/0/0
new file mode 100644
index 000000000..53e30b1bb
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/1/0
new file mode 100644
index 000000000..6ce6be213
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/2/0
new file mode 100644
index 000000000..c1d7e3a50
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/3/0
new file mode 100644
index 000000000..9a951a2eb
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/4/0
new file mode 100644
index 000000000..364bd3055
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/5/0
new file mode 100644
index 000000000..6ad24bfb2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/6/0
new file mode 100644
index 000000000..f2ad79c13
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/7/0
new file mode 100644
index 000000000..2304744d4
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/8/0
new file mode 100644
index 000000000..6a4b7bcda
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/9/0
new file mode 100644
index 000000000..91b2fddd2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_CSQ/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/.zarray
new file mode 100644
index 000000000..a138477d1
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<i4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/.zattrs
new file mode 100644
index 000000000..2b09b7a75
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Approximate read depth; some reads may have been filtered"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/0
new file mode 100644
index 000000000..1ee9f9409
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/1
new file mode 100644
index 000000000..e464895f1
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/2
new file mode 100644
index 000000000..ee5f8b2e5
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/3
new file mode 100644
index 000000000..4feb63345
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/4
new file mode 100644
index 000000000..d62192a9f
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/5
new file mode 100644
index 000000000..5bd42723a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/6
new file mode 100644
index 000000000..f416092bd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/7
new file mode 100644
index 000000000..2c7ad0500
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/8
new file mode 100644
index 000000000..9fed735f8
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/9
new file mode 100644
index 000000000..dba6a9c8f
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_DP/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/.zarray
new file mode 100644
index 000000000..7dd93fb45
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|i1",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/.zattrs
new file mode 100644
index 000000000..455e68d3f
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "n-fold degeneracy"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/0
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/1
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/2
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/3
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/4
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/5
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/6
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/7
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/8
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/9
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/.zarray
new file mode 100644
index 000000000..eb78fd611
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/.zarray
@@ -0,0 +1,25 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|O",
+    "fill_value": null,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/.zattrs
new file mode 100644
index 000000000..442261f1b
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Additional information about custom degeneracy annotation:"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/0
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/1
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/2
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/3
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/4
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/5
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/6
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/7
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/8
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/9
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Degeneracy_Info/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/.zarray
new file mode 100644
index 000000000..7dd93fb45
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|i1",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/.zattrs
new file mode 100644
index 000000000..289b06ff4
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Stop position of the interval"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/0
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/1
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/2
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/3
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/4
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/5
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/6
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/7
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/8
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/9
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_END/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/.zarray
new file mode 100644
index 000000000..eb78fd611
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/.zarray
@@ -0,0 +1,25 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|O",
+    "fill_value": null,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/.zattrs
new file mode 100644
index 000000000..160c25f27
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "EST-SFS input"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/0
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/1
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/2
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/3
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/4
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/5
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/6
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/7
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/8
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/9
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_input/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/.zarray
new file mode 100644
index 000000000..eb78fd611
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/.zarray
@@ -0,0 +1,25 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|O",
+    "fill_value": null,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/.zattrs
new file mode 100644
index 000000000..c0d3c74ed
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "EST-SFS probabilities"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/0
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/1
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/2
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/3
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/4
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/5
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/6
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/7
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/8
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/9
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_EST_SFS_probs/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/.zarray
new file mode 100644
index 000000000..618055d22
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<f4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/.zattrs
new file mode 100644
index 000000000..a252a66fb
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Phred-scaled p-value for exact test of excess heterozygosity"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/0
new file mode 100644
index 000000000..a3979785a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/1
new file mode 100644
index 000000000..61c854d30
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/2
new file mode 100644
index 000000000..d6e0e584b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/3
new file mode 100644
index 000000000..2ea806a63
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/4
new file mode 100644
index 000000000..deee51289
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/5
new file mode 100644
index 000000000..3a9aa23e4
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/6
new file mode 100644
index 000000000..6c9afa636
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/7
new file mode 100644
index 000000000..c06a16b38
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/8
new file mode 100644
index 000000000..b4f54b2ee
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/9
new file mode 100644
index 000000000..7995d7a19
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ExcessHet/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/.zarray
new file mode 100644
index 000000000..618055d22
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<f4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/.zattrs
new file mode 100644
index 000000000..3696c95b7
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Phred-scaled p-value using Fisher's exact test to detect strand bias"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/0
new file mode 100644
index 000000000..0f83034bd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/1
new file mode 100644
index 000000000..40921a777
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/2
new file mode 100644
index 000000000..86777435a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/3
new file mode 100644
index 000000000..6d92c0826
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/4
new file mode 100644
index 000000000..f456a0742
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/5
new file mode 100644
index 000000000..9b7777284
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/6
new file mode 100644
index 000000000..2efe5a68a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/7
new file mode 100644
index 000000000..e2bbd4eab
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/8
new file mode 100644
index 000000000..2e67f51c4
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/9
new file mode 100644
index 000000000..e85650ae8
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_FS/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/.zarray
new file mode 100644
index 000000000..618055d22
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<f4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/.zattrs
new file mode 100644
index 000000000..06c22c0ea
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/0
new file mode 100644
index 000000000..f4c423743
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/1
new file mode 100644
index 000000000..0e6a63f94
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/2
new file mode 100644
index 000000000..f4b98d261
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/3
new file mode 100644
index 000000000..09a1d0ee8
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/4
new file mode 100644
index 000000000..a7362bb40
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/5
new file mode 100644
index 000000000..95524b26b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/6
new file mode 100644
index 000000000..c52318d5e
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/7
new file mode 100644
index 000000000..eec95529f
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/8
new file mode 100644
index 000000000..1bb73618f
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/9
new file mode 100644
index 000000000..ac1c8ce0c
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_InbreedingCoeff/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/.zarray
new file mode 100644
index 000000000..56df8e061
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/.zarray
@@ -0,0 +1,23 @@
+{
+    "chunks": [
+        1000,
+        1
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<i2",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        1
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/.zattrs
new file mode 100644
index 000000000..079da3d95
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "alt_alleles"
+    ],
+    "description": "Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/0/0
new file mode 100644
index 000000000..8d4396977
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/1/0
new file mode 100644
index 000000000..13c2ab4c9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/2/0
new file mode 100644
index 000000000..fce892442
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/3/0
new file mode 100644
index 000000000..c6fb571d4
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/4/0
new file mode 100644
index 000000000..126c276ae
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/5/0
new file mode 100644
index 000000000..20c5aa12b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/6/0
new file mode 100644
index 000000000..2765dc1c1
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/7/0
new file mode 100644
index 000000000..d767e59f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/8/0
new file mode 100644
index 000000000..fec389514
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/9/0
new file mode 100644
index 000000000..d8eea4da3
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAC/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/.zarray
new file mode 100644
index 000000000..2d0713a90
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/.zarray
@@ -0,0 +1,23 @@
+{
+    "chunks": [
+        1000,
+        1
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<f4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        1
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/.zattrs
new file mode 100644
index 000000000..715c4e28b
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "alt_alleles"
+    ],
+    "description": "Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/0/0
new file mode 100644
index 000000000..d752a72e5
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/1/0
new file mode 100644
index 000000000..e07ee177f
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/2/0
new file mode 100644
index 000000000..0634c3bd5
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/3/0
new file mode 100644
index 000000000..c4eb72c2d
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/4/0
new file mode 100644
index 000000000..ec9150c98
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/5/0
new file mode 100644
index 000000000..9ab081e6a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/6/0
new file mode 100644
index 000000000..a9af60b18
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/7/0
new file mode 100644
index 000000000..88e237991
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/8/0
new file mode 100644
index 000000000..89fc0f92d
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/9/0
new file mode 100644
index 000000000..c4ee428c7
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MLEAF/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/.zarray
new file mode 100644
index 000000000..618055d22
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<f4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/.zattrs
new file mode 100644
index 000000000..eb558f227
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "RMS Mapping Quality"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/0
new file mode 100644
index 000000000..0e571f13f
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/1
new file mode 100644
index 000000000..c62ec79de
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/2
new file mode 100644
index 000000000..072234def
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/3
new file mode 100644
index 000000000..4f12abfbe
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/4
new file mode 100644
index 000000000..54c8386a0
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/5
new file mode 100644
index 000000000..afa40daef
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/6
new file mode 100644
index 000000000..3a9ac8906
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/7
new file mode 100644
index 000000000..f222351b6
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/8
new file mode 100644
index 000000000..98fd68df7
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/9
new file mode 100644
index 000000000..6985db31c
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQ/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/.zarray
new file mode 100644
index 000000000..618055d22
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<f4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/.zattrs
new file mode 100644
index 000000000..d26c78a03
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/0
new file mode 100644
index 000000000..abddcd11a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/1
new file mode 100644
index 000000000..73d537893
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/2
new file mode 100644
index 000000000..e15aa786e
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/3
new file mode 100644
index 000000000..eee58b0ed
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/4
new file mode 100644
index 000000000..1b9df4445
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/5
new file mode 100644
index 000000000..2cc7643a0
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/6
new file mode 100644
index 000000000..bfd05cc68
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/7
new file mode 100644
index 000000000..930fee3bb
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/8
new file mode 100644
index 000000000..dd62ed439
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/9
new file mode 100644
index 000000000..bd673a819
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_MQRankSum/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/.zarray
new file mode 100644
index 000000000..618055d22
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<f4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/.zattrs
new file mode 100644
index 000000000..c7be7a399
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Variant Confidence/Quality by Depth"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/0
new file mode 100644
index 000000000..de76438bd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/1
new file mode 100644
index 000000000..cfe395dc4
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/2
new file mode 100644
index 000000000..ac95e42dd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/3
new file mode 100644
index 000000000..ac7748019
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/4
new file mode 100644
index 000000000..780e3b56a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/5
new file mode 100644
index 000000000..35d3dfc9e
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/6
new file mode 100644
index 000000000..3afe26422
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/7
new file mode 100644
index 000000000..dd0addf67
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/8
new file mode 100644
index 000000000..932dcb5c3
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/9
new file mode 100644
index 000000000..be1f779ee
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_QD/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/.zarray
new file mode 100644
index 000000000..f373d4af4
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/.zarray
@@ -0,0 +1,23 @@
+{
+    "chunks": [
+        1000,
+        2
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|i1",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        2
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/.zattrs
new file mode 100644
index 000000000..69df24023
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "INFO_RAW_MQandDP_dim"
+    ],
+    "description": "Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation."
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/0/0
new file mode 100644
index 000000000..ed597f0cd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/1/0
new file mode 100644
index 000000000..ed597f0cd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/2/0
new file mode 100644
index 000000000..ed597f0cd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/3/0
new file mode 100644
index 000000000..ed597f0cd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/4/0
new file mode 100644
index 000000000..ed597f0cd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/5/0
new file mode 100644
index 000000000..ed597f0cd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/6/0
new file mode 100644
index 000000000..ed597f0cd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/7/0
new file mode 100644
index 000000000..ed597f0cd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/8/0
new file mode 100644
index 000000000..ed597f0cd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/9/0
new file mode 100644
index 000000000..ed597f0cd
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_RAW_MQandDP/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/.zarray
new file mode 100644
index 000000000..618055d22
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<f4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/.zattrs
new file mode 100644
index 000000000..50e043cfc
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/0
new file mode 100644
index 000000000..f6d2b1053
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/1
new file mode 100644
index 000000000..40a55c0a8
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/2
new file mode 100644
index 000000000..f1417f059
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/3
new file mode 100644
index 000000000..36a5d6454
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/4
new file mode 100644
index 000000000..d738ba4ce
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/5
new file mode 100644
index 000000000..616ea8984
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/6
new file mode 100644
index 000000000..4e98f9e2e
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/7
new file mode 100644
index 000000000..96654ff7e
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/8
new file mode 100644
index 000000000..43c4d7817
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/9
new file mode 100644
index 000000000..495076ebf
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_ReadPosRankSum/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/.zarray
new file mode 100644
index 000000000..618055d22
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<f4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/.zattrs
new file mode 100644
index 000000000..462e09a58
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/0
new file mode 100644
index 000000000..93c94ac8c
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/1
new file mode 100644
index 000000000..039cb7da4
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/2
new file mode 100644
index 000000000..271da8e29
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/3
new file mode 100644
index 000000000..95b287e28
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/4
new file mode 100644
index 000000000..9c7f39669
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/5
new file mode 100644
index 000000000..9c437ea5a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/6
new file mode 100644
index 000000000..10e81cd52
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/7
new file mode 100644
index 000000000..6e38e74a7
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/8
new file mode 100644
index 000000000..365aa505e
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/9
new file mode 100644
index 000000000..57b5e641f
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_SOR/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/.zarray
new file mode 100644
index 000000000..7dd93fb45
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|i1",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/.zattrs
new file mode 100644
index 000000000..bdfd4e3ef
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Whether coding site is synonymous"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/0
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/1
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/2
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/3
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/4
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/5
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/6
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/7
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/8
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/9
new file mode 100644
index 000000000..132fa164b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/.zarray
new file mode 100644
index 000000000..eb78fd611
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/.zarray
@@ -0,0 +1,25 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|O",
+    "fill_value": null,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/.zattrs
new file mode 100644
index 000000000..819a91025
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Additional information about custom synonymy annotation:"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/0
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/1
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/2
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/3
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/4
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/5
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/6
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/7
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/8
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/9
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_Synonymy_Info/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/.zarray
new file mode 100644
index 000000000..fa9aa9312
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/.zarray
@@ -0,0 +1,27 @@
+{
+    "chunks": [
+        1000,
+        2
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|O",
+    "fill_value": null,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        10000,
+        2
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/.zattrs
new file mode 100644
index 000000000..202af6237
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "alleles"
+    ],
+    "description": "List of the reference and alternate alleles"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/0/0
new file mode 100644
index 000000000..850081282
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/1/0
new file mode 100644
index 000000000..f88237293
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/2/0
new file mode 100644
index 000000000..49ef223c9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/3/0
new file mode 100644
index 000000000..4546c59ec
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/4/0
new file mode 100644
index 000000000..f42c3e37a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/5/0
new file mode 100644
index 000000000..48da3f51f
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/6/0
new file mode 100644
index 000000000..c82dabaac
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/7/0
new file mode 100644
index 000000000..65d9c61f1
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/8/0
new file mode 100644
index 000000000..7b410e5a5
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/9/0
new file mode 100644
index 000000000..9b76b6ed1
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_allele/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/.zarray
new file mode 100644
index 000000000..8d42cfc5e
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<i2",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/.zattrs
new file mode 100644
index 000000000..bfd867f57
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "An identifier from the reference genome or an angle-bracketed ID string pointing to a contig in the assembly file"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/0
new file mode 100644
index 000000000..85e3219fa
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/1
new file mode 100644
index 000000000..85e3219fa
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/2
new file mode 100644
index 000000000..85e3219fa
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/3
new file mode 100644
index 000000000..85e3219fa
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/4
new file mode 100644
index 000000000..08a79f230
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/5
new file mode 100644
index 000000000..2079c19b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/6
new file mode 100644
index 000000000..2079c19b2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/7
new file mode 100644
index 000000000..f4f8f922f
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/8
new file mode 100644
index 000000000..652c419e9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/9
new file mode 100644
index 000000000..652c419e9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_contig/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/.zarray
new file mode 100644
index 000000000..f32d17a20
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/.zarray
@@ -0,0 +1,23 @@
+{
+    "chunks": [
+        1000,
+        7
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 2
+    },
+    "dimension_separator": "/",
+    "dtype": "|b1",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000,
+        7
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/.zattrs
new file mode 100644
index 000000000..116fb890b
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/.zattrs
@@ -0,0 +1,7 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants",
+        "filters"
+    ],
+    "description": "Filter status of the variant"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/0/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/0/0
new file mode 100644
index 000000000..ec305e088
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/0/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/1/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/1/0
new file mode 100644
index 000000000..ec305e088
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/1/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/2/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/2/0
new file mode 100644
index 000000000..ec305e088
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/2/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/3/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/3/0
new file mode 100644
index 000000000..ec305e088
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/3/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/4/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/4/0
new file mode 100644
index 000000000..ec305e088
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/4/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/5/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/5/0
new file mode 100644
index 000000000..ec305e088
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/5/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/6/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/6/0
new file mode 100644
index 000000000..ec305e088
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/6/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/7/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/7/0
new file mode 100644
index 000000000..ec305e088
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/7/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/8/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/8/0
new file mode 100644
index 000000000..ec305e088
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/8/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/9/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/9/0
new file mode 100644
index 000000000..ec305e088
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_filter/9/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/.zarray
new file mode 100644
index 000000000..eb78fd611
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/.zarray
@@ -0,0 +1,25 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|O",
+    "fill_value": null,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/.zattrs
new file mode 100644
index 000000000..809c8bbac
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "resources/reference/genome.corrected.gff.gz (overlap)"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/0
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/1
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/2
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/3
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/4
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/5
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/6
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/7
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/8
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/9
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_genome.corrected.gff.gz/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/.zarray
new file mode 100644
index 000000000..eb78fd611
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/.zarray
@@ -0,0 +1,25 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|O",
+    "fill_value": null,
+    "filters": [
+        {
+            "id": "vlen-utf8"
+        }
+    ],
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/.zattrs
new file mode 100644
index 000000000..d6fb72c29
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "List of unique identifiers where applicable"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/0
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/1
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/2
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/3
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/4
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/5
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/6
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/7
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/8
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/9
new file mode 100644
index 000000000..2cfac38f9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/.zarray
new file mode 100644
index 000000000..739c1e722
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 2
+    },
+    "dimension_separator": "/",
+    "dtype": "|b1",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/.zattrs
new file mode 100644
index 000000000..bdafca1d9
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": ""
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/0
new file mode 100644
index 000000000..00a735f78
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/1
new file mode 100644
index 000000000..00a735f78
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/2
new file mode 100644
index 000000000..00a735f78
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/3
new file mode 100644
index 000000000..00a735f78
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/4
new file mode 100644
index 000000000..00a735f78
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/5
new file mode 100644
index 000000000..00a735f78
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/6
new file mode 100644
index 000000000..00a735f78
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/7
new file mode 100644
index 000000000..00a735f78
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/8
new file mode 100644
index 000000000..00a735f78
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/9
new file mode 100644
index 000000000..00a735f78
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_id_mask/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/.zarray
new file mode 100644
index 000000000..7dd93fb45
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "|i1",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/.zattrs
new file mode 100644
index 000000000..a7cfdf454
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "The length of the variant measured in bases"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/0
new file mode 100644
index 000000000..0251fcc77
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/1
new file mode 100644
index 000000000..0251fcc77
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/2
new file mode 100644
index 000000000..0251fcc77
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/3
new file mode 100644
index 000000000..0251fcc77
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/4
new file mode 100644
index 000000000..0251fcc77
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/5
new file mode 100644
index 000000000..0251fcc77
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/6
new file mode 100644
index 000000000..0251fcc77
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/7
new file mode 100644
index 000000000..0251fcc77
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/8
new file mode 100644
index 000000000..0251fcc77
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/9
new file mode 100644
index 000000000..0251fcc77
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_length/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/.zarray
new file mode 100644
index 000000000..a138477d1
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<i4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/.zattrs
new file mode 100644
index 000000000..768fff2dd
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "The reference position"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/0
new file mode 100644
index 000000000..1f881d202
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/1
new file mode 100644
index 000000000..d0d19d0b5
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/2
new file mode 100644
index 000000000..198bb3a26
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/3
new file mode 100644
index 000000000..e7cc5a5d5
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/4
new file mode 100644
index 000000000..2a8ca848b
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/5
new file mode 100644
index 000000000..6aa45f3fc
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/6
new file mode 100644
index 000000000..a6908833a
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/7
new file mode 100644
index 000000000..289579c99
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/8
new file mode 100644
index 000000000..08a926362
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/9
new file mode 100644
index 000000000..2c7ab8a61
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_position/9 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/.zarray b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/.zarray
new file mode 100644
index 000000000..618055d22
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/.zarray
@@ -0,0 +1,21 @@
+{
+    "chunks": [
+        1000
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 7,
+        "cname": "zstd",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dimension_separator": "/",
+    "dtype": "<f4",
+    "fill_value": null,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        10000
+    ],
+    "zarr_format": 2
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/.zattrs b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/.zattrs
new file mode 100644
index 000000000..ab7da0cc6
--- /dev/null
+++ b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/.zattrs
@@ -0,0 +1,6 @@
+{
+    "_ARRAY_DIMENSIONS": [
+        "variants"
+    ],
+    "description": "Phred-scaled quality score"
+}
\ No newline at end of file
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/0 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/0
new file mode 100644
index 000000000..729e00090
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/0 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/1 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/1
new file mode 100644
index 000000000..dc52761d9
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/1 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/2 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/2
new file mode 100644
index 000000000..09ab63223
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/2 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/3 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/3
new file mode 100644
index 000000000..f1346208e
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/3 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/4 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/4
new file mode 100644
index 000000000..42b86dfc2
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/4 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/5 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/5
new file mode 100644
index 000000000..58a9d9643
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/5 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/6 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/6
new file mode 100644
index 000000000..242b48b0e
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/6 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/7 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/7
new file mode 100644
index 000000000..df4369fdc
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/7 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/8 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/8
new file mode 100644
index 000000000..4b2f66088
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/8 differ
diff --git a/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/9 b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/9
new file mode 100644
index 000000000..39eaaad64
Binary files /dev/null and b/resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz/variant_quality/9 differ
diff --git a/testing/test_annotation.py b/testing/test_annotation.py
index 73cbd3ba4..dfa0cad51 100644
--- a/testing/test_annotation.py
+++ b/testing/test_annotation.py
@@ -3436,3 +3436,30 @@ def test_n_samples_target_sites_argument(self):
         counts = np.array([list(v._monomorphic_samples.values()) for k, v in anc.items()]) / n_target_sites
 
         self.assertLessEqual(np.max(np.var(counts, axis=0)), 1e-4)
+
+
+class ZarrAnnotationTestCase(TestCase):
+    """
+    Test the annotators using Zarr backend.
+    """
+
+    def test_run_inference_full_betula_dataset(self):
+        anc = fd.MaximumLikelihoodAncestralAnnotation(
+            outgroups=["ERR2103730", "ERR2103731"],
+            n_ingroups=10,
+            prior=None,
+            model=fd.K2SubstitutionModel(),
+            parallelize=True
+        )
+
+        ann = fd.Annotator(
+            vcf="resources/genome/betula/biallelic.with_outgroups.subset.10000.vcz",
+            output='scratch/test_get_likelihood_full_betula_dataset_zarr.vcf',
+            annotations=[anc],
+            max_sites=10000,
+        )
+        ann.annotate()
+
+        anc.to_est_sfs("resources/EST-SFS/test-betula-biallelic-100000.txt")
+
+        self.assertEqual(anc.evaluate_likelihood(anc.params_mle), anc.likelihood)