Vcftools Weir-Fst-Pop

Question

[Rubal7]

Hi all,

Could anyone provide a quick example command line for the VCFtools option --weir-fst-pop that will run? When I try I get an error that --weir-fst-pop is an unrecognized command. I am trying to calculate Fst between 2 vcf files using the Weir and Cockerham method.

Thanks very much for your help.

Answer 1

[Adam]

If vcftools is telling you the --weir-fst-pop isn't recognized, it's probably indicating that you're using an old version of vcftools. The command --weir-fst-pop was only introduced in version 0.1.9

The correct usage is:

./vcftools --vcf vcf_file1.vcf --weir-fst-pop individual_list_1.txt --weir-fst-pop individual_list_2.txt

[Rubal7]

solves it thanks!

Answer 2

[Zev.Kronenberg]

Hi Rubal7,

The documentation leads me to believe that you can only use 1 file:

--weir-fst-pop <filename>

I have written a Weir and Cockerham Fst calculator, but you need a CDR file (in the VAAST pipeline). I would be happy to share it with you.