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Revision as of 02:13, 11 September 2015
, 02:13, 11 September 2015→Full List of Options
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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>]
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| <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).
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| <font face=Courier>--chr 22</font>
| <font face=Courier>--chr 22</font>
