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29 bytes removed
, 23:59, 5 March 2016
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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 0x70C | + | Skip records with any of the specified flags set, default 0xF0C |
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| 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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| * fails QC checks | | * fails QC checks |
| * duplicate | | * duplicate |
− | | + | * supplementary |
− | This parameter was added in version 1.0.10.
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| === Mark entirely clipped reads as unmapped (<code>--unmapped</code>)=== | | === Mark entirely clipped reads as unmapped (<code>--unmapped</code>)=== |