Question: Calculating Fst for Multiallelic variants in VCFs
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gravatar for ma17
6 months ago by
ma170
ma170 wrote:

Hi,

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?

Thanks

fst multiallelic vcf • 293 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by ma170

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 6 months ago by RamRS20k
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