Minimac3 Cookbook : Converting Files to VCF: Difference between revisions

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Created page with " Consequently, we would have the following steps. ===Convert GWAS Panel Files into VCF === If pre-phased GWAS data is available in VCF format, users can skip this step. Othe..."
 
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= Introduction =


Consequently, we would have the following steps.
This wiki-page explains the main tools available to convert other format files to VCF format.


===Convert GWAS Panel Files into VCF ===
= Convert '''PLINK''' 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.
Use PLINK2 (available [https://www.cog-genomics.org/plink2 here]) as follows:
 
* '''PLINK:''' Use PLINK2 (available [https://www.cog-genomics.org/plink2 here]) as follows:


  plink --bfile Gwas.Chr20.Phased.Output \
  plink --bfile Gwas.Chr20.Phased.Output \
Line 12: Line 11:
       --out Gwas.Chr20.Phased.Output.VCF.format
       --out Gwas.Chr20.Phased.Output.VCF.format


* '''MaCH:''' Use Mach2VCF (coming soon) as follows:
= 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


* '''SHAPEIT:''' Use SHAPEIT (available [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download here]) as follows:
= 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


=== Download Reference Panel ===
= 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]]


Commonly used reference panels are 1000 Genomes Phase 3 (2,535 samples), 1000 Genomes Phase 1 (1,094 samples), HapMap2 (269 samples), Haplotype Reference Consortium (32,914 samples) etc. Users are advised to use either 1000 Genomes Phase 3 (available for download in [[#Reference Panels for Download |Reference Panels ]]) or the Haplotype Reference Consortium (which due to data privacy issues cannot be shared publicly but can be used for imputation remotely on a server through a [http://imputationserver.sph.umich.edu/ imputation server] setup at University of Michigan). Reference panels for different versions of 1000 Genomes, in both VCF and <code>M3VCF</code> format, are available for download in [[#Reference Panels for Download |Reference Panels]].
* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')


=== Impute Samples ===
* [[Minimac3 Cookbook : Pre-Phasing | Pre-Phasing ]]


The final step for imputation involves running '''Minimac3''' to perform the imputation analysis. Now that we have the pre-phased GWAS panel (in VCF format) and the appropriate reference panel (in VCF or <code>M3VCF</code> format), we can run Minimac3 as follows. In the following examples, the first one uses a VCF file for reference (that can be obtained as explained above) and the second example uses a <code>M3VCF</code> file (that might have been downloaded from the links [[#Reference Panels for Download|below]] or created on a previous run of Minimac3).
* [[Minimac3 Cookbook : Converting Files to VCF| Converting Files to VCF]]


../bin/Minimac3 --refHaps ReferencePanel.Chr20.1000Genomes.vcf \
= Contact =
                --haps Gwas.Chr20.Phased.Output.VCF.format.vcf \
                --prefix Gwas.Chr20.Imputed.Output


../bin/Minimac3 --refHaps ReferencePanel.Chr20.1000Genomes.m3vcf \
In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].
                --haps Gwas.Chr20.Phased.Output.VCF.format.vcf \
                --prefix Gwas.Chr20.Imputed.Output

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:

Contact

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

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