Calculating Fst for Multiallelic variants in VCFs

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

vcf fst multiallelic

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written 7.9 years ago by ma17 •

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.

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written 7.9 years ago by Ram

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