Question: Pairwise Fst between populations using vcftools
gravatar for MC
4.3 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 • 4.3k views
ADD COMMENTlink modified 23 months ago by mellissa.demille30 • written 4.3 years ago by MC10

So, what do you want?

ADD REPLYlink written 3.8 years ago by nottwya10
gravatar for mellissa.demille
23 months ago by
mellissa.demille30 wrote:

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

ADD COMMENTlink written 23 months ago by mellissa.demille30
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