vcftools –weir-fst-pop returns -nan
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.
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