Minimac3 Cookbook : Converting Files to VCF

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This wiki-page explains the main tools available 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 (available here) 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:

  • Converting Files to VCF


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