I would like to obtain the Weir & Cockerham Fst for single SNPs from my vcf files for wished populations.
I thought to use vcftools as it seemd to be straight forward, however it only gives me the 'mean Fst' and 'weighted Fst' for all SNPs in my file.
I used the following command:
vcftools --vcf my.vcf --weir-fst-pop pop1.txt --weir-fst-pop pop2.txt
Is there any way to make vcftools to give me a list with all single Fst values???