Difference between revisions of "Minimac3 Cookbook : Converting Files to VCF"
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= Convert '''MaCH''' Files = | = Convert '''MaCH''' Files = | ||
| − | Use Mach2VCF ( | + | Use Mach2VCF (available [ftp://share.sph.umich.edu/minimac3/Mach2VCF.v1.Source.Binary.tar.gz here]) as follows: |
mach2VCF --haps Gwas.Chr20.Phased.Output.hap \ | mach2VCF --haps Gwas.Chr20.Phased.Output.hap \ | ||
Latest revision as of 23:32, 30 January 2015
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.
