Using BCFtools to obtain between population Fst values from vcf file
0
1
Entering edit mode
4.4 years ago
ishengomae ▴ 110

I'm at a point where I would want to compute between population Weir and Cockerham Fst values directly from a large vcf file. Apparently VCFtools had utilities for this as in this question http://seqanswers.com/forums/showthread.php?t=34511 and the command were if I am correct:

vcftools --vcf input_file.vcf --weir-fst-pop Population1.txt --weir-fst-pop Population2.txt > Weir_Cockerham_fst.txt

How would I compute the same thing with BCFtools?

Thanks.

Fst Weir and Cockerham BCFtools vcf SNP • 2.2k views
ADD COMMENT

Login before adding your answer.

Traffic: 1816 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6