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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
By default skips reads with any of the following flags set:
By default skips reads with any of the following flags set:
* fails QC checks
* fails QC checks
* duplicate
* duplicate
* supplementary
=== Mark entirely clipped reads as unmapped (<code>--unmapped</code>)===
=== Mark entirely clipped reads as unmapped (<code>--unmapped</code>)===
