Minimac3 Cookbook : Converting Files to VCF

Introduction

After the pre-phasing has been done, we can begin to run the imputation. But before that, we need to convert our phased GWAS panel files (obtained above) to VCF format (since Minimac3 can only use VCF format files). If pre-phased GWAS data is available in VCF format, users can skip this step. Otherwise, the following steps show how to convert other format files to VCF format.

Convert PLINK Files

Use PLINK2 (available here) as follows:

plink --bfile Gwas.Chr20.Phased.Output \
      --recode vcf \
      --out Gwas.Chr20.Phased.Output.VCF.format

Convert MaCH Files

Use Mach2VCF (coming soon) as follows:

mach2VCF --haps Gwas.Chr20.Phased.Output.hap \
         --snps Gwas.Chr20.Phased.Output.snps \
         --prefix Gwas.Chr20.Phased.Output.VCF.format

Convert SHAPEIT Files

Use SHAPEIT (available here) as follows:

shapeit -convert \
        --input-haps Gwas.Chr20.Phased.Output \
        --output-vcf Gwas.Chr20.Phased.Output.VCF.format.vcf

Useful Wiki Pages

There are a few pages in this Wiki that may be useful to for Minimac3 users. Here are links to a few:

• Minimac3 Overview Page

• Minimac3 Imputation Cookbook (Recommended for New Users!!)

• Pre-Phasing

• Converting Files to VCF

Contact

In case of any queries and bugs please contact Sayantan Das.