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*<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>--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>--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.
*<code>--TrimAlleles</code> indicates whether to trim alleles and variants IDs to 100 characters. Since PLINK does not allow variant IDs longer than 16,000 characters, this option can be used if variant names are too long
= 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].
