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
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written
by
wmelroy827 •
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.
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written
by
chrchang523
Hi, what would be a good --vcf-min-gp cut off value? 0.85 or higher or lower?
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