Minimac3 Cookbook : Converting Files to VCF
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Introduction
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:
- Minimac3 Imputation Cookbook (Recommended for New Users!!)
Contact
In case of any queries and bugs please contact Sayantan Das.