Changes

For the pseudo-autosomal region (PAR) on chromosome X, no extra parameter is necessary. For the non-PAR region, please ensure the following:

For the pseudo-autosomal region (PAR) on chromosome X, no extra parameter is necessary. For the non-PAR region, please ensure the following:

* 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 diploids''', then just add handle <code>--samePoidy</code>. This will NOT generate sex information in the output PLINK <code>.fam</code> file.

** If you still need 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.

** If you still need the sex column in <code>.fam</code> file to be correctly updated, then supply a sex file using <code>--sexFile SomeFile</code> where <code>SomeFile</code> has two columns: the first columns has the names of samples as found in the VCF file, the second columns has M or F.

* 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. However, if no GT tags are available, you would need to supply te sex file as above.

* If your input VCF dosage file has '''males as haploids''' and '''also has GT information''', the tool with automatically determine sex of the samples and report them in the output <code>.fam</code> file. However, if no GT tags are available, you would need to supply the sex file as described above.

= Command Line Options =

= Command Line Options =