Pairwise Fst between populations using vcftools

Question

[MC]

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

[nottwya]

So, what do you want?

Answer 1

[mellissa.demille]

the .log file gives you a total fst between the two pops