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DosageConvertor (view source)

Revision as of 14:01, 18 January 2019

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= Introduction =
 
= Introduction =
 
DosageConvertor is a C++ tool to convert dosage files (in VCF format) from [[Minimac4| Minimac3/4]] to other formats such as MaCH or PLINK.
 
DosageConvertor is a C++ tool to convert dosage files (in VCF format) from [[Minimac4| Minimac3/4]] to other formats such as MaCH or PLINK.
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[Please note that this tool CANNOT handle missing values in the input files and may NOT work appropriately for non-Minimac3/4 VCF files]
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= Download =
 
= Download =
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[https://github.com/Santy-8128/DosageConvertor DosageConvertor - Github]  
 
[https://github.com/Santy-8128/DosageConvertor DosageConvertor - Github]  
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| Source Files
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[ftp://share.sph.umich.edu/minimac3/DosageConvertor/DosageConvertor.v1.0.3.tar.gz  UNIX Users ]
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| Binary Executable <sup>&#8224;</sup>
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(Ubuntu 4.8.4)
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[ftp://share.sph.umich.edu/minimac3/DosageConvertor/DosageConvertorExecutable.tar.gz  UNIX Users ]
      
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'''<sup>&#8224;</sup>''' Binary executables are NOT guaranteed to run on every LINUX machine. Please compile from source files if you have trouble with the executable, or clone from the [https://github.com/Santy-8128/DosageConvertor github repository]. Else contact the author [mailto:sayantan@umich.edu Sayantan Das].
      
= Installation =
 
= Installation =
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  ## EXTRACT M3VCFTOOLS AND COMPILE
 
  ## EXTRACT M3VCFTOOLS AND COMPILE
 
  &nbsp;
 
  &nbsp;
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  wget ftp://share.sph.umich.edu/minimac3/DosageConvertor/DosageConvertor.v1.0.3.tar.gz
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  git clone https://github.com/Santy-8128/DosageConvertor
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tar -xzvf DosageConvertor.v1.0.3.tar.gz
   
  cd DosageConvertor/
 
  cd DosageConvertor/
 
  make
 
  make
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== Convert to MaCH Files ==
 
== Convert to MaCH Files ==
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The following command will convert an input VCF dosage file to a MaCH/minimac dosage file (the format for previous versions of [[Minimac | minimac]]). The generated dosage files can be tested for association using [http://genome.sph.umich.edu/wiki/Mach2dat:_Association_with_MACH_output mach2dat].  
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The following command will convert an input VCF dosage file to a MaCH/minimac dosage file (the format for previous versions of [[Minimac | minimac]]). The generated dosage files can be tested for association using tools like [http://genome.sph.umich.edu/wiki/Mach2dat:_Association_with_MACH_output mach2dat] or [http://www.genabel.org/packages/ProbABEL ProbABEL].  
    
  ./DosageConvertor        --vcfDose      TestDataImputedVCF.dose.vcf.gz
 
  ./DosageConvertor        --vcfDose      TestDataImputedVCF.dose.vcf.gz
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