Difference between revisions of "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 [https://www.cog-genomics.org/plink2 here]) as follows: | |
− | |||
− | |||
plink --bfile Gwas.Chr20.Phased.Output \ | plink --bfile Gwas.Chr20.Phased.Output \ | ||
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--out Gwas.Chr20.Phased.Output.VCF.format | --out Gwas.Chr20.Phased.Output.VCF.format | ||
− | + | = Convert '''MaCH''' Files = | |
+ | |||
+ | 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 \ | ||
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--prefix Gwas.Chr20.Phased.Output.VCF.format | --prefix Gwas.Chr20.Phased.Output.VCF.format | ||
− | + | = Convert '''SHAPEIT''' Files = | |
+ | |||
+ | Use SHAPEIT (available [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download here]) as follows: | ||
shapeit -convert \ | shapeit -convert \ | ||
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--output-vcf Gwas.Chr20.Phased.Output.VCF.format.vcf | --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| Minimac3 Overview Page]] | ||
− | + | * [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''') | |
− | + | * [[Minimac3 Cookbook : Pre-Phasing | Pre-Phasing ]] | |
− | + | * [[Minimac3 Cookbook : Converting Files to VCF| Converting Files to VCF]] | |
− | + | = Contact = | |
− | |||
− | |||
− | + | In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das]. | |
− | |||
− |
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.