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== Converting Chromosome X Files ==
== Converting Chromosome X Files ==
For a minimac3/4 output file containing the pseudo-autosomal region (PAR) on chromosome X, no extra parameter is necessary. For files containing the non-PAR region, please ensure the following:
For conversion of X chromosome files from minimac3/4, please ensure the following:
* If your input VCF dosage file has '''males as diploids''', then just add handle <code>--allDiploid</code>. This will NOT generate sex information in the output PLINK <code>.fam</code> file. You would have to update it manually.
* If your input VCF dosage file has '''males as diploids''', then just add handle <code>--allDiploid</code>. This will NOT generate sex information in the output PLINK <code>.fam</code> file.
* If your input VCF dosage file has '''males as haploids''' and '''also has GT information''', the tool with automatically determine the sex of the samples and report them in the output <code>.fam</code> file. No extra parameters are required.
** 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:
** If GT tags are NOT available, you would need to supply the sex file as described in the section below. Otherwise it will throw an error.
*** the first column has the sample names as found in the VCF file
** '''NOTE''': If your VCF file has males as haploids, do NOT use <code>--allDiploid</code> as the code would NOT throw any error, but the output results would be erroneous.
*** the second columns has M (for males) or F (for females).
* If your input VCF dosage file has '''males as haploids''' and '''also has GT information''', the tool with automatically determine the sex of the samples from their ploidy and report them in the output <code>.fam</code> file. No extra parameters are required.
** If '''GT''' tags are NOT available, you would need to supply the <code>--sexFile</code> as described above. Otherwise it will throw an error.
** '''NOTE''': If your VCF file has males as haploids, do NOT use <code>--allDiploid</code> as the output results would be erroneous (although the code would NOT throw any error)
= Command Line Options =
= Command Line Options =
