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The command options for DosageConvertor are explained below.
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 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 some missing columns.
*<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>--prefix</code> denotes the output file prefix (default value: <code>Converted.Dosage</code>).
*<code>--prefix</code> denotes the output file prefix (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 handles: <code>plink</code> (default) and <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> 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>--format</code> decides the format of the 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>).
*<code>--idDelimiter</code> denotes the delimiter to Split VCF Sample ID into FID and IID for PLINK format (default value <code>_</code>).
*<code>--idDelimiter</code> denotes the delimiter to Split VCF Sample ID into FID and IID for PLINK format.
*<code>--allDiploid</code> denotes whether to assume all samples are diploids. If this handle is on, the output PLINK <code>.fam</code> will NOT contain any sex information.
*<code>--allDiploid</code> denotes whether to assume all samples are diploids (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>--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.
*<code>--TrimAlleles</code> denotes whether to trim length of alleles and variants IDs since PLINK does NOT allow really long character sequences.
