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*<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>--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>--prefix</code> sets the prefix for output files (default value: <code>Converted.Dosage</code>)
*<code>--type</code> denotes the output file format (available options: <code>plink</code> (default) or <code>mach</code>)
*<code>--type</code> 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 (<code>DS</code>: default), genotype probabilities (<code>GP</code>), or hard genotypes calls (<code>GT</code>) from the input VCF file
*<code>--tag</code> indicates whether to import imputed values from dosages (<code>DS</code>: default), genotype probabilities (<code>GP</code>), or hard genotype 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> sets the format of the converted output file.
*<code>--buffer</code> denotes the number of markers to import at a time (valid only for MaCH format) (default value <code>10000</code>).
**If <code>--type mach</code> is used, <code>--format</code> can take values 1, 2, or 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])
*<code>--idDelimiter</code> denotes the delimiter to Split VCF Sample ID into FID and IID for PLINK format.
**If <code>--type mach</code> is used, <code>--format</code> can take values 1 or 2. Details are given in [[#Convert to MaCH Files| Convert to MaCH Files]]
*<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>--buffer</code> sets the number of markers to import at a time (MaCH format only) (default value <code>10000</code>)
*<code>--idDelimiter</code> denotes the delimiter character used to split '''VCF Sample ID''' into '''FID''' and '''IID''' for PLINK format
*<code>--allDiploid</code> denotes whether to assume all samples are 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>--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.
