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, 13:19, 27 September 2011
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| --out : the SAM/BAM file to be written | | --out : the SAM/BAM file to be written |
| Optional Parameters: | | Optional Parameters: |
− | --refFile : reference file name used to convert any bases that match the reference to '-' | + | --refFile : reference file name used to convert any bases that match the reference to '=' |
| --keepOQ : keep the OQ tag rather than removing it. Default is to remove it. | | --keepOQ : keep the OQ tag rather than removing it. Default is to remove it. |
| --keepDups : keep duplicates rather than removing records marked duplicate. Default is to remove them. | | --keepDups : keep duplicates rather than removing records marked duplicate. Default is to remove them. |
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| --params : print the parameter settings | | --params : print the parameter settings |
| </pre> | | </pre> |
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| | | |
| = Usage = | | = Usage = |