Negative Fst values from VCFtools result
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3.8 years ago
nitinra ▴ 50

Hello all,

I am calculating Fst using VCFtools and here is the code I am running:

vcftools --vcf input.vcf --weir-fst-pop pop1.txt --weir-fst-pop pop2.txt --out pop1_pop2

I am getting the mean fst value in negative: -0.0003 (I did expect it to be low since they are very close), but a lot of the loci has negative values in the pop1_pop2.weir. I know that negative Fst is meaningless, so is there a reason why vcftools has values in the negative? Can I remove those negative value loci and recalculate Fst using awk? Thank you!

SNP genome vcftools fst • 1.7k views
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