Question: convert imputed genotypes in VCF file to plink format
1
gravatar for wmelroy827
4.9 years ago by
wmelroy82710
United States
wmelroy82710 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 • 5.7k views
ADD COMMENTlink modified 4.9 years ago by chrchang5235.6k • written 4.9 years ago by wmelroy82710
1
gravatar for chrchang523
4.9 years ago by
chrchang5235.6k
United States
chrchang5235.6k 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 COMMENTlink written 4.9 years ago by chrchang5235.6k

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

ADD REPLYlink written 3.1 years ago by Floris Brenk890
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1750 users visited in the last hour