75
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Converting Chromosome X Files
* 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>--samePloidy</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 names of samples as found in the VCF file, 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.
