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| | <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> |
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| | <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> |
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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 </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> |
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| |- | | |- |
| | <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> |
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| | <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> |