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Minimac3 Cookbook : Converting Files to VCF (view source)

Revision as of 23:32, 30 January 2015

212 bytes removed ,  23:32, 30 January 2015
→‎Convert MaCH Files
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= Introduction =
 
= Introduction =
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After the pre-phasing has been done, we can begin to run the imputation. But before that, we need to convert our phased GWAS panel files (obtained above) to VCF format (since Minimac3 can only use VCF format 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.
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This wiki-page explains the main tools available to convert other format files to VCF format.
    
= Convert '''PLINK''' Files =  
 
= Convert '''PLINK''' Files =  
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= Convert '''MaCH''' Files =  
 
= Convert '''MaCH''' Files =  
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Use Mach2VCF (coming soon) as follows:
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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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