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Revision as of 19:34, 6 June 2016
, 19:34, 6 June 2016→Full List of Options
= Introduction =
[http://genome.sph.umich.edu/wiki/Minimac3 '''Minimac3 '''] is a lower memory and more computationally efficient implementation of [http://genome.sph.umich.edu/wiki/Minimac2 minimac2]. It is an algorithm for genotypic imputation that works on phased genotypes (say from [http://genome.sph.umich.edu/wiki/MaCH MaCH]) and is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.
This wiki page gives users '''a full list of all the available options on Minimac3'''.
= 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. 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.
The following table gives a brief description of all the parameters of '''Minimac3'''. A detailed description would be available soon.
{| 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 =
'''Minimac3 ''' is available as an undocumented release version. The source files (and binary executable) are available for download in [[Minimac3#Download | Source Files]] and commonly used reference panels in VCF and <font face=Courier>M3VCF</font> formats are available for download in [[Minimac3#Reference Panels for Download | Reference Panels]].
= Useful Wiki Pages =
There are a few pages in this Wiki that may be useful to for '''Minimac3''' users. Here are links to a few:
* [[Minimac3| Minimac3 Overview Page]]
* [[Minimac3 Usage | Minimac3 Usage and Documentation]]
* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')
* [[Minimac3 Examples| Minimac3 Examples]]
* [[M3VCF Files| M3VCF Files]]
= Contact =
In case of any queries and bugs please contact [mailto:sayantan@umich.edu Sayantan Das].
