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Revision as of 21:18, 1 December 2016
, 21:18, 1 December 2016no edit summary
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| <font face=Courier>--vcfOutput</font>
| <font face=Courier>--vcfOutput</font>
| If ON, imputed data will NOT be output as VCF output file [Default: ON].
| If ON, imputed data will NOT be output as VCF output file [Default: ON]
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| <font face=Courier>--doseOutput</font>
| <font face=Courier>--doseOutput</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]
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| <font face=Courier>--<s>hapOutput</s></font>
| <font face=Courier>--<s>hapOutput</s></font>
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| <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,HDS </font>. <font face=Courier>GT</font> stands for Genotype, <font face=Courier>DS</font> stands for genotype dosage, <font face=Courier>HDS</font> stands for haplotype dosage and <font face=Courier>GP</font> stands for genotype probabilities [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,HDS</font>. <font face=Courier>GT</font> stands for Genotype, <font face=Courier>DS</font> stands for genotype dosage, <font face=Courier>HDS</font> stands for haplotype dosage and <font face=Courier>GP</font> stands for genotype probabilities [Default: <font face=Courier>GT,DS</font>]
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| <font face=Courier>--allTypedSites</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).
| 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]
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| <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]
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| <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]
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| <font face=Courier>--chr 22</font>
| <font face=Courier>--chr 22</font>
