Question: Minimac3 VCF to .gen and .sample format
gravatar for Caragh
14 months ago by
Caragh 40
Caragh 40 wrote:

Hi there,

I imputed some genotype data using the Michigan imputation server and got the output in VCF format. This is the first time I have used this server and I'm struggling to figure out how to handle the data.

Is there a way to convert the VCF files into .gen and .sample files whilst retaining info scores?

Many thanks,


.gen snp minimac3 imputation • 1.1k views
ADD COMMENTlink modified 14 months ago by chrchang5234.8k • written 14 months ago by Caragh 40
gravatar for chrchang523
14 months ago by
United States
chrchang5234.8k wrote:

If the VCF only has dosage information ("DS"), this is possible with recent plink 2.0 alpha builds (which you can get from ):

plink2 --vcf minimac_output.vcf dosage=DS --export oxford --out new_fileset_prefix

However, if the VCF file contains genotype probabilities ("GP") and you want to preserve them, you may need to write your own script for this.

ADD COMMENTlink written 14 months ago by chrchang5234.8k
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