487
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchMinimac3 - Full List of Options (view source)
Revision as of 19:34, 6 June 2016
, 19:34, 6 June 2016→Full List of Options
| <font face=Courier>--refHaps filename </font>
| <font face=Courier>--refHaps filename </font>
| VCF file or <font face=Courier>M3VCF</font> file containing haplotype data for reference panel.
| VCF file or <font face=Courier>M3VCF</font> file containing haplotype data for reference panel.
|-
| <font face=Courier>--rsid</font>
| This option only imports RS ID of variants from ID column of reference file (if available).
|-
|-
| <font face=Courier>--passOnly</font>
| <font face=Courier>--passOnly</font>
| <font face=Courier>--nobgzip</font>
| <font face=Courier>--nobgzip</font>
| If ON, output files will be NOT bgzipped.
| If ON, output files will be NOT bgzipped.
|-
| <font face=Courier>--vcfOutput</font>
| If ON, imputed data will NOT be output as VCF output file [Default: ON].
|-
|-
| <font face=Courier>--doseOutput</font>
| <font face=Courier>--doseOutput</font>
| <font face=Courier>--help</font>
| <font face=Courier>--help</font>
| A short help on options.
| A short help on options.
|-
| <font face=Courier>--lowMemory</font>
| If ON, a low memory version of Minimac3 will be run.
|-
|-
| <font face=Courier>--cpus 5</font>
| <font face=Courier>--cpus 5</font>
