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Revision as of 21:11, 1 December 2016
, 21:11, 1 December 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 '''Minimac4'''. Users should see the wiki-page on [[Minimac4 Usage | Minimac4 Usage and Documentation]] and [[Minimac4 Imputation Cookbook]] for further help on how to use these options.
The following table gives a brief description of all the parameters of '''Minimac4'''. New handles added in Minimac4 are highlighted in bold.
Users should see the wiki-page on [[Minimac4 Usage | Minimac4 Usage and Documentation]] and [[Minimac4 Imputation Cookbook]] for further help on how to use these options.
{| border="1" cellpadding="2"
{| border="1" cellpadding="2"
| Prefix for all output files generated. By default: <font face=Courier>[Minimac3.Output]</font>
| Prefix for all output files generated. By default: <font face=Courier>[Minimac3.Output]</font>
|-
|-
| <font face=Courier>--updateModel</font>
| <font face=Courier>--<s>updateModel</s></font>
| If ON, saved parameter estimates read from a M3VCF file will be further updated using the gwas samples. Will be ignored if VCF reference file. [Default: OFF]
| This parameter has been disabled in Minimac4
|-
|-
| <font face=Courier>--nobgzip</font>
| <font face=Courier>--nobgzip</font>
| If ON, imputed data will be output as dosage file as well [Default: OFF].
| If ON, imputed data will be output as dosage file as well [Default: OFF].
|-
|-
| <font face=Courier>--hapOutput</font>
| <font face=Courier>--<s>hapOutput</s></font>
| If ON, phased imputed data will be output as well [Default: OFF].
| This parameter has been disabled in Minimac4
|-
|-
| <font face=Courier>--format</font>
| <font face=Courier>--format</font>
