Hi there,
I would like to obtain the Weir & Cockerham Fst for single SNPs from my vcf files for wished populations.
I thought to use vcftools as it seemd to be straight forward, however it only gives me the 'mean Fst' and 'weighted Fst' for all SNPs in my file.
I used the following command:
vcftools --vcf my.vcf --weir-fst-pop pop1.txt --weir-fst-pop pop2.txt
Is there any way to make vcftools to give me a list with all single Fst values???
Thx, Felix
2 answers
Problem solved with the help of Adam Auton via the vcftools-mailing list.
Apparently if --out is not specified (as in my case) there is automatically a out.weir.fst created in the current directory. By specifying --out you can set a certain path/name to the out file.
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