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8 bytes added, 19:09, 11 July 2017
Command Line Options
*<code>--info</code> is the info file generated by minimac3/4 at the same time as the VCF dosage file. This parameter is optional, but if NO info file is provided, the output MaCH info file will have missing columns
*<code>--prefix</code> sets the prefix for output files (default value: <code>Converted.Dosage</code>)
*<code>--type</code> denotes sets the output file format (available options: <code>plink</code> (default) or <code>mach</code>)*<code>--tag</code> indicates whether to import imputed values from dosage dosages (<code>DS</code>: default), genotype probabilities (<code>GP</code>), or hard genotypes genotype calls (<code>GT</code>) from the input VCF file*<code>--format</code> decides sets the format of the converted output file. **If <code>--type mach</code> is used, <code>--format</code> can take values 1, 2 and , or 3. Each of these values correspond to the three different formats available for PLINK dosage files (details given [ here]). **If <code>--type mach</code> is used, <code>--format</code> can only take values 1 and or 2. Details are given in [[#Convert to MaCH Files| Convert to MaCH Files]] *<code>--buffer</code> denotes sets the number of markers to import at a time (valid only for MaCH formatonly) (default value <code>10000</code>). *<code>--idDelimiter</code> denotes the delimiter character used to Split split '''VCF Sample ID ''' into '''FID ''' and '''IID ''' for PLINK format.*<code>--allDiploid</code> denotes whether to assume all samples are diploids diploid (necessary for chromosome X). If this handle is on, the output PLINK <code>.fam</code> will NOT contain any sex information.
*<code>--sexFile</code> denotes the sex file which should have two columns: the first column has the sample names as found in the VCF file, and the second columns has M (for males) or F (for females).
*<code>--TrimAlleles</code> denotes whether to trim length of alleles and variants IDs since PLINK does NOT allow really long character sequences.

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