Vcftools Fst Calculation For Single Snps

Question

[klimklam]

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

Answer 1

[Adam]

These are contained in an output file with the suffix '.weir.fst'.

Answer 2

[klimklam]

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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.

Best