Am trying to calculate pairwise Fst between populations with my SNP data in a .vcf file using vcftools-0.1.14. The output I get is a list of all SNPs with their respective Fst estimates, which is not what I want.
This is the command I am running for populations:
./vcftools --vcf vcf_file.vcf --weir-fst-pop individual_list_1.txt --weir-fst-pop individual_list_2.txt --weir-fst-pop individual_list_n.txt
Could someone help? Thanks