Changes

== Convert to MaCH Files ==

== Convert to MaCH Files ==

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].  

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].  

  ./DosageConvertor        --vcfDose      TestDataImputedVCF.dose.vcf.gz

  ./DosageConvertor        --vcfDose      TestDataImputedVCF.dose.vcf.gz

                           --format      1                              (or 2)

                           --format      1                              (or 2)

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.

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</code> and <code>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</code> and <code>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 inputting the info file using <code>--info</code> is optional. 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 ==