Calculating Fst for Multiallelic variants in VCFs

Question

[ma17]

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

[Ram]

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.