vcftools –weir-fst-pop returns -nan

vcftools –weir-fst-pop returns -nan

0

I am trying to calculate per site Fst for two samples in a vcf file but am getting -nan for the output for the mean Fst estimate and for every site. This is what I ran:

vcftools --gzvcf ${VCF} --weir-fst-pop DBFCU --weir-fst-pop BBMCU --out ./cu_pops

The output from the run is:

    VCFtools - 0.1.16
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
    --gzvcf /panfs/pfs.local/scratch/sjmac/e284e911/variantcalling/WildPops_combined.vcf.gz
    --weir-fst-pop DBFCU
    --weir-fst-pop BBMCU
    --keep DBFCU
    --keep BBMCU
    --out ./cu_pops

Using zlib version: 1.2.11
Warning: Expected at least 2 parts in INFO entry: ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
Warning: Expected at least 2 parts in INFO entry: ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
Keeping individuals in 'keep' list
After filtering, kept 2 out of 9 Individuals
Outputting Weir and Cockerham Fst estimates.
Weir and Cockerham mean Fst estimate: -nan
Weir and Cockerham weighted Fst estimate: -nan
After filtering, kept 1886530 out of a possible 1886530 Sites
Run Time = 26.00 seconds

Thanks for any assistance.


fst


vcftools

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