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= Full List of Options =
= Full List of Options =
The following table gives a brief description of all the parameters of '''Minimac4'''. New handles added in Minimac4 are highlighted in bold.
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.
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.
| 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>--<s>updateModel</s></font>
| <font face=Courier>'''--<s>updateModel</s>'''</font>
| This parameter has been disabled in Minimac4
| This parameter has been disabled in Minimac4
|-
|-
| If ON, output files will be NOT bgzipped.
| If ON, output files will be NOT bgzipped.
|-
|-
| <font face=Courier>--vcfBuffer 200</font>
| <font face=Courier>--'''vcfBuffer 200'''</font>
| This is number of samples to be stored in the memory before writing a VCF file piece
| This is number of samples to be stored in the memory before writing a VCF file piece
|-
|-
| 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>--<s>hapOutput</s></font>
| <font face=Courier>'''--<s>hapOutput</s>'''</font>
| This parameter has been disabled in Minimac4
| This parameter has been disabled in Minimac4
|-
|-
| 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). [Default: OFF]
| 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). [Default: OFF]
|-
|-
| <font face=Courier>--meta</font>
| <font face=Courier>'''--meta'''</font>
| If this handle is ON, Minimac4 also outputs some diagnostic measures required for meta-imputation by MetaMinimac. Please turn this handle ON if you plan to use MetaMinimac later for meta-imputation of dosages from Minimac4. [Default: OFF]
| If this handle is ON, Minimac4 also outputs some diagnostic measures required for meta-imputation by MetaMinimac. Please turn this handle ON if you plan to use MetaMinimac later for meta-imputation of dosages from Minimac4. [Default: OFF]
|-
|-
| <font face=Courier>--memUsage</font>
| <font face=Courier>'''--memUsage'''</font>
| If this handle is ON, Minimac4 will NOT run the imputation, but instead report an estimated memory usage summary. It will also report some minor instructions to change the memory usage by tweaking parameters in the command line. This summary might enable users to get an idea of memory consumption and modify it, if need be, before starting the imputation experiment. [Default: OFF]
| If this handle is ON, Minimac4 will NOT run the imputation, but instead report an estimated memory usage summary. It will also report some minor instructions to change the memory usage by tweaking parameters in the command line. This summary might enable users to get an idea of memory consumption and modify it, if need be, before starting the imputation experiment. [Default: OFF]
|-
|-
