From Genome Analysis Wiki
→Command Line Options
*<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> 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> indicates whether to trim
length of alleles and variants IDs since PLINK does NOT allow really long character sequences.
= Contact =
In case of any queries and bugs please contact [mailto:firstname.lastname@example.org Sayantan Das].