Question: Calculating Fst for Multiallelic variants in VCFs
gravatar for ma17
16 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 • 634 views
ADD COMMENTlink modified 16 months ago • written 16 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 16 months ago by RamRS25k
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