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No extra parameter is necessary for converting chromosome X on the pseudo-autosomal region. For the non-PAR region:
No extra parameter is necessary for converting chromosome X on the pseudo-autosomal region. For the non-PAR region:
* If your input VCF dosage file has males as haploids and also has GT information, the tool with automatically determine sex of the sample and report in the in the output <code>.fam</code> file
* If your input VCF dosage file has males as diploids, then just add handle <code>--samePoidy</code>. This will not generate sex information in the output PLINK <code>.map</code> file.
* If your input VCF dosage file has males as haploids and also has GT information, the tool with automatically determine sex of the sample and report in the in the output <code>.fam</code> file.
* If your input VCF file does NOT have GT information or as males coded as diploids, and you would still like the sex column in <code>.fam</code> file to be updated, then supply a sex file using <code>--sexFile SomeFile</code> where <code>SomeFile</code> has two columns, the names of samples as found in the VCF file as the first column, and M or F in the second column.
= Command Line Options =
= Command Line Options =
