No sites retained when using -sites

[partridc]

Hello,

I know this issue has been mentioned before, but I have not been able to resolve the problem based on others approaches. I have a list of pruned SNPs with major/minor allele information that I am trying to include to create a covariance matrix for a PCA. It seems the list has been indexed correctly:

$ cat -A HWA.allpops.post.cutoff09.1Mb.LDpruned_snps.noheader.noJBJKT.list
CM099565.1^I1001134^IA^IT$
CM099565.1^I1003230^IG^IT$
CM099565.1^I1006284^IC^IT$
CM099565.1^I1008660^IG^IT$
CM099565.1^I10130368^IA^IT$
CM099565.1^I10132927^IG^IT$
CM099565.1^I10133188^IC^IA$
CM099565.1^I10144991^IC^IT$
CM099565.1^I10145607^IG^IT$
CM099565.1^I1017011^IC^IT$

It also states that the correct number of chromosome are being read and that the major/minor allele information is present.
-> [prep_sites.cpp] Reading binary representation of '/mnt/projects/partridc_project/HWA/results/HWA.allpops.post.cutoff09.1Mb.LDpruned_snps.noheader.noJBJKT.list
-> [prep_sites.cpp] nChr: 10 loaded from binary filter file
-> Filterfile contains major/minor information
-> [abcFilter.cpp] -sites is still beta, use at own risk...

I double checked to make sure that these positions are included in the original maf files that are created without the -site option, and they are all listed with the correct alleles.

However, when I run angsd with the -site option, it states that 0 sites are retained.

    -> Total number of sites analyzed: 211519930
    -> Number of sites retained after filtering: 0
    [ALL done] cpu-time used =  24301.15 sec
    [ALL done] walltime used =  24466.00 sec

I'm currently using angsd version: 0.941-26-g6b5d906 (htslib: 1.23-5-g1274083f) build(Jan 21 2026 14:22:14). I know that there was a previous issue related to the anaconda version which I was initially using, so I reinstalled it from github.

The code I'm using is:

SNPLIST=$BASEDIR/results/HWA.allpops.post.cutoff09.1Mb.LDpruned_snps.noheader.noJBJKT.list

./angsd -b $BASEDIR/sample_lists/full.good.bam2.txt -ref $REF -anc $REF -out $BASEDIR/results/HWA.post.cutoff09.LDpruned.modtutorial.PCA
-GL 2 -doGLF 2 -doPost 1
-doMajorMinor 4 -doMaf 1
-doIBS 1 -doCounts 1 -doCov 1 -makeMatrix 1 -sites $SNPLIST

Any suggestions on what I may be doing wrong would be greatly appreciated. Thank you!

[partridc]

For anyone else having this issue, it seems like angsd 0.940 is working with the -sites option.
https://github.com/ANGSD/angsd/releases/tag/0.940