Pairwise Fst between populations using vcftools

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

snp next-gen

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updated 7.9 years ago by mellissa.demille •

• written 10.3 years ago by MC •

So, what do you want?

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written 9.8 years ago by nottwya •

1 answer

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

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written 7.9 years ago by mellissa.demille •

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