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, 18:09, 12 March 2015
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| --overlapsOnly : Only output overlapping read pairs | | --overlapsOnly : Only output overlapping read pairs |
| --excludeFlags : Skip records with any of the specified flags set, default 0x70C | | --excludeFlags : Skip records with any of the specified flags set, default 0x70C |
− | --noeof : Do not expect an EOF block on a bam file.
| + | --unmapped : Mark records that would be completely clipped as unmapped |
| + | --noeof : Do not expect an EOF block on a bam file. |
| --params : Print the parameter settings to stderr | | --params : Print the parameter settings to stderr |
| Clipping By Coordinate Optional Parameters: | | Clipping By Coordinate Optional Parameters: |