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
= Full List of Options =
= Full List of Options =
The following table gives a brief description of all the parameters of '''Minimac3'''. A more detailed description would be available soon.
The following table gives a brief description of all the parameters of '''Minimac3'''. A more detailed description would be available soon. Users should see the wiki-page on [[Minimac3 Usage | Minimac3 Usage and Documentation]] and [[Minimac3 Imputation Cookbook]] for further help on how to use these options.
{| border="1" cellpadding="2"
{| border="1" cellpadding="2"
| <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>--format</font>
| <font face=Courier>--format</font>
| Specifies which fields to output for the FORMAT field in output VCF file. Available handles: <font face=Courier>GT,DS,GP </font>[Default: <font face=Courier>GT,DS</font>].
| Specifies which fields to output for the FORMAT field in output VCF file. Available handles: <font face=Courier>GT,DS,GP </font>[Default: <font face=Courier>GT,DS</font>]
|-
| <font face=Courier>--allTypedSites</font>
| Also Includes variants that were genotyped but NOT in the reference panel in the output files (and imputes any missing data in such variants to the major allele frequency).
|-
|-
| <font face=Courier>--chr 22</font>
| <font face=Courier>--chr 22</font>
|-
|-
| <font face=Courier>--window 5000</font>
| <font face=Courier>--window 5000</font>
| Length of buffer region on either side of <font face=Courier>--start</font> and <font face=Courier>--end</font>. By default = 0.
| Length of buffer region (in bp units) on either side of <font face=Courier>--start</font> and <font face=Courier>--end</font>. By default = 500000 (if chunking is done) and = 0 (if no chunking is being done).
|-
|-
| <font face=Courier>--rec</font>
| <font face=Courier>--rec</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>
| Percentage probability of sending SUCCESS/FAILURE status of the execution to home server [Default: 50%]
| Percentage probability of sending SUCCESS/FAILURE status of the execution to home server [Default: 50%]
|}
|}
= Download =
= Download =
