75
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Command Line Options
sets the format of the converted output file:
sets the format of the converted output file:
*If <code>--type plink</code> is used, <code>--format</code> can take values 1, 2, or 3. Each of these values correspond to the three different formats available for PLINK dosage files (details given [http://www.cog-genomics.org/plink/1.9/assoc#dosage here])
*If <code>--type plink</code> is used, <code>--format</code> can take values 1, 2, or 3.
*If <code>--type mach</code> is used, <code>--format</code> can take values 1 or 2. Details are given in [[#Convert to MaCH Files| Convert to MaCH Files]]
Each of these values correspond to the three different formats available for PLINK dosage files (details given [http://www.cog-genomics.org/plink/1.9/assoc#dosage here])
*If <code>--type mach</code> is used, <code>--format</code> can take values 1 or 2.
Details are given in [[#Convert to MaCH Files| Convert to MaCH Files]]
|-
|-
| <code>--buffer</code>
| <code>--buffer</code>
| <code>--allDiploid</code>
| <code>--allDiploid</code>
|
|
indicates whether to assume all samples are diploid (necessary for chromosome X). If this option is active, the output PLINK <code>.fam</code> will NOT contain any sex information
indicates whether to assume all samples are diploid (necessary for chromosome X).
If this option is active, the output PLINK <code>.fam</code> will NOT contain any sex information
|-
|-
| <code>--sexFile</code>
| <code>--sexFile</code>
|
|
indicates a file containing sample sex information, which requires two columns: the first column contains the sample names as found in the VCF file, and the second columns contains either M (for males) or F (for females)
indicates a file containing sample sex information, which requires two columns:
*the first column contains the sample names as found in the VCF file
*the second columns contains either M (for males) or F (for females)
|-
|-
| <code>--TrimAlleles</code>
| <code>--TrimAlleles</code>
|
|
indicates whether to trim alleles and variants IDs to 100 characters. Since PLINK does not allow variant IDs longer than 16,000 characters, this option can be used if variant names are too long
indicates whether to trim alleles and variants IDs to 100 characters
Since PLINK does not allow variant IDs longer than 16,000 characters, this option can be used if variant names are too long.
|}
|}
