Minimac3 VCF to .gen and .sample format

Question

[Caragh]

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,

Caragh

Answer 1

[chrchang523]

If the VCF only has dosage information ("DS"), this is possible with recent plink 2.0 alpha builds (which you can get from https://www.cog-genomics.org/plink/2.0/ ):

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.