Question

vcftools filter Allele frequency for polyploid variants

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6.7 years ago

Cindy ▴ 60

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

sequencing • 2.1k views

ADD COMMENT • link updated 3.3 years ago by alexanderkaier • 0 • written 6.7 years ago by Cindy ▴ 60

score 0 · Answer 1 · 2021-01-08

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Entering edit mode

3.3 years ago

alexanderkaier • 0

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

ADD COMMENT • link 3.3 years ago by alexanderkaier • 0