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DosageConvertor (view source)

Revision as of 17:56, 11 July 2017

337 bytes added ,  17:56, 11 July 2017
→‎Convert to MaCH Files
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== Convert to MaCH Files ==
 
== Convert to MaCH Files ==
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The following command line should convert a input VCF dosage file to a MaCH/minimac dosage file (the format that available in the earlier version 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 line should convert a input VCF dosage file to a MaCH/minimac dosage file (the format that was available in the earlier 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].  
    
  ./DosageConvertor        --vcfDose      TestDataImputedVCF.dose.vcf.gz
 
  ./DosageConvertor        --vcfDose      TestDataImputedVCF.dose.vcf.gz
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                           --info        TestDataImputedVCF.info (NOT mandatory)
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                           --info        TestDataImputedVCF.info         (NOT mandatory)
 
                           --prefix      OutPrefix
 
                           --prefix      OutPrefix
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                           --type        plink
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                           --type        mach
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                           --format      1
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                           --format      1                               (or 2)
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This command line would create three files :  <code> OutPrefix.plink.dosage.gz, OutPrefix.fam, OutPrefix.map </code>. The <code>--format</code> parameter can take values 1, 2 and 3. Each of these values correspond to the three different formats available for PLINK dosage files (details on PLINK dosage files are given [http://www.cog-genomics.org/plink/1.9/assoc#dosage here]). Note that the generated <code>OutPrefix.map</code> does NOT contain any phenotype information (which needs to be manually edited before PLINK can run association testing).
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When <code>--type mach</code> is used, the <code>--format</code> parameter can only take values 1 and 2. If the value is 1, the code generates <code> OutPrefix.mach.dose.gz, OutPrefix.info</code> where <code>OutPrefix.mach.dose.gz</code> contains the expected alternate allele count (one value per sample per marker). If the value is 2, it generates <code> OutPrefix.mach.gprob.gz, OutPrefix.info</code> where <code>OutPrefix.mach.gprob.gz</code> contains the genotype likelihoods for reference homozygote and heterozygote  (two values per sample per marker). Note that in the input <code>--info</code> is NOT mandatory. However, if this info file is NOT provided, the output <code>OutPrefix.info</code> file will have some empty columns. Thus, if available, the generated info file should be provided along with the VCF file as input.
    
== Converting Chromosome X Files ==
 
== Converting Chromosome X Files ==
Santy.8128
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