vcftools filter Allele frequency for polyploid variants

Question

[Cindy]

Hi all, I have vcf files for mitochondrial DNA, which is polyploid. I want to filter out some variants based on the AF. I tried vcftools, it showed not supported. Anyone knows how to do that?

Appreciate ahead

Answer 1

[alexanderkaier]

vcflib and within that the vcffilter program can be used to filter polyploid VCF files. Unfortunately, vcftools does not support polyploidy.