Open main menu

Genome Analysis Wiki β



73 bytes added, 19:24, 11 July 2017
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 to 100 characters. Since PLINK does NOT not allow really variant IDs longer than 16,000 characters, this option can be used if variant names are too long character sequences.
= Contact =
In case of any queries and bugs please contact [ Sayantan Das].