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**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]]
**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>--buffer</code> sets the number of markers to import at a time (MaCH format only) (default value <code>10000</code>)
*<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>--idDelimiter</code> indicates 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>--allDiploid</code> indicates whether to assume all samples are diploid (necessary for chromosome X). If this option is active, 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> indicates a file containing sample sex information, which requires two columns: the first column contains the sample names as found in the VCF file, and the second columns contains either 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> indicates whether to trim length of alleles and variants IDs since PLINK does NOT allow really long character sequences.
= Contact =
= Contact =
In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].
In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].
