Question: Calculating Fst for Multiallelic variants in VCFs
gravatar for ma17
19 months ago by
ma1710 wrote:


I have a vcf file composed of multiallelic variants and I'm trying to calculate Fst between populations. Vcftools --weir-fst-pop only calculates fst for biallelic variants. Is there a tool that can directly calculate fst for multiallelic variants using vcf files?


fst multiallelic vcf • 704 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by ma1710

Have you considered normalizing the VCF so you'd have multiple biallelic records for a multi-allelic variant? It also has the side effect of addressing many other VCF irregularities.

ADD REPLYlink written 19 months ago by RamRS26k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1836 users visited in the last hour