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Question: convert imputed genotypes in VCF file to plink format
2
gravatar for wmelroy827
6.1 years ago by
wmelroy827 • 20
United States
wmelroy827 • 20 wrote:

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
plink imputed genotypes vcf • 6.9k views
ADD COMMENT • link •
modified 6.1 years ago by chrchang523 ♦ 7.6k • written 6.1 years ago by wmelroy827 • 20
2
gravatar for chrchang523
6.1 years ago by
chrchang523 ♦ 7.6k
United States
chrchang523 ♦ 7.6k wrote:

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.
ADD COMMENT • link written 6.1 years ago by chrchang523 ♦ 7.6k

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

ADD REPLY • link written 4.4 years ago by Floris Brenk • 970
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