Changes

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 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:

* If your input VCF dosage file has '''males as diploids''', then just add handle <code>--samePloidy</code>. This will NOT generate sex information in the output PLINK <code>.fam</code> file.

* 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 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 column has the sample names as found in the VCF file, and the second columns has M (for males) or F (for females).

** 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 column has the sample names as found in the VCF file, and 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 and report them in the output <code>.fam</code> file. No extra parameters are required.

* 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 GT tags are NOT available, you would need to supply the sex file as described above. Otherwise it will throw an error.

** If GT tags are NOT available, you would need to supply the sex file as described above. Otherwise it will throw an error.

** '''NOTE''': If your VCF file has males as haploids, do NOT use <code>--samePloidy</code> as the code would NOT throw any error, but the output results would be erroneous.

** '''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.

= Command Line Options =

= Command Line Options =