Question: Pairwise Fst between populations using vcftools
gravatar for MC
3.0 years ago by
MC10 wrote:

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 • 2.6k views
ADD COMMENTlink modified 7 months ago by mellissa.demille10 • written 3.0 years ago by MC10

So, what do you want?

ADD REPLYlink written 2.5 years ago by nottwya10
gravatar for mellissa.demille
7 months ago by
mellissa.demille10 wrote:

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

ADD COMMENTlink written 7 months ago by mellissa.demille10
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