convert imputed genotypes in VCF file to plink format

Question

[wmelroy827]

Hello,

I have imputed data (genotype dosages) in a VCF file and would like to force hard genotype calls and then convert to PLINK file format. Any ideas on how to do this? Thanks,

Whitney

Answer 1

[chrchang523]

If your VCF file has genotype dosages on a 0-1 scale in the GP field, recent PLINK 1.9 builds support

plink --vcf [vcf filename] --vcf-min-gp [hard call threshold] --out [output file prefix]

See https://www.cog-genomics.org/plink2/input#vcf for a few more VCF filtering options.

[Floris Brenk]

Hi, what would be a good --vcf-min-gp cut off value? 0.85 or higher or lower?