Question: Vcftools Weir-Fst-Pop
2
gravatar for Rubal7
7.4 years ago by
Rubal7770
Rubal7770 wrote:

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.

vcf genome vcftools fst • 7.1k views
ADD COMMENTlink modified 6.3 years ago by Biostar ♦♦ 20 • written 7.4 years ago by Rubal7770
3
gravatar for Adam
7.4 years ago by
Adam990
United States
Adam990 wrote:

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
ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by Adam990

solves it thanks!

ADD REPLYlink written 7.4 years ago by Rubal7770
0
gravatar for Zev.Kronenberg
7.4 years ago by
United States
Zev.Kronenberg11k wrote:

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.

ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by Zev.Kronenberg11k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 3245 users visited in the last hour