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| 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: |
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− | * 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. |
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| = Command Line Options = | | = Command Line Options = |