Release v1.5.2

DNAscope LongRead

• Add support for population vcf input
• Fix a bug where RepeatModel output was not used correctly

Release v1.5.1

General updates

• Add a --version argument

DNAscope Hybrid

• Add support for population vcf input

Pangenome

• Check that the kmc executable supports reading from stdin

Release v1.5.0

General updates

• Use exec instead of the shell to run commands
• Update the bcftools dependency of most pipelines to v1.22, which allows for simultaneous vcf generation and indexing.
• Update the packaging version.

Pangenome

• Introduce a new pipeline, sentieon-pangenome for accelerated alignment to the pangenome graph. This pipeline replaces the earlier pangenome pipeline with vg giraffe alignment.

DNAscope LongRead

• Updates to vcf_mod.py to fix the RPA annotation.
• Add -L to minimap2 commands to handle alignments with very long CIGAR strings.

DNAscope Hybrid

• With --rgsm, completely replace readgroups during variant calling.

Release v1.4.0

General updates

• Terminate running jobs gracefully after receiving a catchable exception (SIGINT and SIGTERM)

Pangenome

Initial alpha/beta implementation of a pangenome alignment and variant calling pipeline. The pangenome pipeline uses vg giraffe for alignment to the pangenome and DNAscope for small variant calling. Please review the pipeline documentation for more information.

Release v1.3.0

General updates

• Add unit and integration tests.
• Simplify the command-line help by hiding some rarely used arguments.
• Add a workaround if lscpu is not available.

DNAscope Hybrid

• Remove the TrimRepeat argument in the hybrid ONT pipeline.
• Require an ONT bundle version > 1.2. Earlier versions of the ONT bundle are trained using the TrimRepeat argument.

Release v1.2.3

General updates

• Refactor all pipelines, removing the external dependency on argh.
• Updates to the test pipelines.

DNAscope Hybrid

• Ensure that readgroups information is passed correctly between functions, fixing a bug in the alignment and variant calling pipeline.

Release v1.2.2

General Updates

• Pipelines now execute in a deterministic order.
• Add support for parsing bundle files.

DNAscope

• Add a new argument --skip_metrics to skip all metrics collection and multiqc.

DNAscope Hybrid

• The pipeline now parses the bundle_info.json file in the hybrid model bundle to determine platform-specific arguments, removing the --longread_tech argument.
• Add a new argument --skip_metrics to skip all short-read metrics, multiqc, and mosdepth.
• Add a new argument --rgsm that can be used to set the SM tag in the input file readgroups.

Release v1.2.1

General updates

• Fix a bug when parsing arguments in older python versions.
• Add support for reading unix ar archive files

DNAscope Hybrid

• Add an additional readgroup tag to long reads in the hybrid pipeline.

Release v1.2.0

General updates

• Add the DNAscope Hybrid pipeline for hybrid short and long-read variant calling from the same sample.
• Use underscores, _, instead of hyphens, -, as a separator in long arguments.
• Use a more flexible method for job scheduling, enabling concurrent execution of jobs.

DNAscope LongRead

• Add CNV calling with hificnv

DNAscope

• Runtime improvements

Release v1.1.0

Updates to the sentieon-cli pipelines

General updates

• Improved logging
• Add a Dockerfile

DNAscope LongRead

• Incorporate mosdepth for alignment QC
• Add haploid gVCF output