75
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Command Line Options
= Command Line Options =
= Command Line Options =
The command options for DosageConvertor are explained below.
*<code>--vcfDose</code> is a mandatory parameter indicating the minimac3/4 VCF dosage file to be converted
*<code>--vcfDose</code> is a mandatory parameter indicating the minimac3/4 VCF dosage file to be converted
*<code>--info</code> is the info file generated by minimac3/4 in the same experiment. This parameter is optional, but if NO info file is provided, the output MaCH info file will have some missing columns.
*<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> denotes the output file prefix (default value: <code>Converted.Dosage</code>).
*<code>--prefix</code> sets the prefix for output files (default value: <code>Converted.Dosage</code>)
*<code>--type</code> denotes the output file format (available handles: <code>plink</code> (default) and <code>mach</code>).
*<code>--type</code> denotes the output file format (available options: <code>plink</code> (default) or <code>mach</code>)
*<code>--tag</code> decides whether to import imputed values from dosage (<code>DS</code>: default), or genotype probabilities (<code>GP</code>), or hard call genotypes (<code>GT</code>) of the input VCF file.
*<code>--tag</code> indicates whether to import imputed values from dosage (<code>DS</code>: default), genotype probabilities (<code>GP</code>), or hard genotypes calls (<code>GT</code>) from the input VCF file
*<code>--format</code> decides the format of the converted output file. If <code>--type mach</code> is used, <code>--format</code> can take values 1, 2 and 3. Each of these values correspond to the three different formats available for PLINK dosage files (details given [http://www.cog-genomics.org/plink/1.9/assoc#dosage here]). If <code>--type mach</code> is used, <code>--format</code> can only take values 1 and 2. Details are given in [[#Convert to MaCH Files| Convert to MaCH Files]]
*<code>--format</code> decides the format of the converted output file. If <code>--type mach</code> is used, <code>--format</code> can take values 1, 2 and 3. Each of these values correspond to the three different formats available for PLINK dosage files (details given [http://www.cog-genomics.org/plink/1.9/assoc#dosage here]). If <code>--type mach</code> is used, <code>--format</code> can only take values 1 and 2. Details are given in [[#Convert to MaCH Files| Convert to MaCH Files]]
*<code>--buffer</code> denotes the number of markers to import at a time (valid only for MaCH format) (default value <code>10000</code>).
*<code>--buffer</code> denotes the number of markers to import at a time (valid only for MaCH format) (default value <code>10000</code>).
