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, 00:15, 6 March 2016
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| and exit when trying to run on an already mark-duplicated BAM | | and exit when trying to run on an already mark-duplicated BAM |
| --excludeFlags <flag> : exclude reads with any of these flags set when determining or marking duplicates | | --excludeFlags <flag> : exclude reads with any of these flags set when determining or marking duplicates |
− | by default (0x304): exclude unmapped, secondary reads, and QC failures | + | by default (0xB04): exclude unmapped, secondary reads, QC failures, and supplementary reads |
| --verbose : Turn on verbose mode | | --verbose : Turn on verbose mode |
| --noeof : Do not expect an EOF block on a bam file. | | --noeof : Do not expect an EOF block on a bam file. |
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| | | |
| === Skip Records with any of the Specified Flags (<code>--excludeFlags</code>)=== | | === Skip Records with any of the Specified Flags (<code>--excludeFlags</code>)=== |
− | Skip records with any of the specified flags set, default 0x304 | + | Skip records with any of the specified flags set, default 0xB04 |
| | | |
| By default skips reads with any of the following flags set: | | By default skips reads with any of the following flags set: |
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| * secondary alignment | | * secondary alignment |
| * fails QC checks | | * fails QC checks |
| + | * supplementary reads |
| | | |
| This parameter was added in version 1.0.10. | | This parameter was added in version 1.0.10. |