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220 bytes added
, 02:13, 11 September 2015
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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> |