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=== Skip Records with any of the Specified Flags (<code>--buildExcludeFlags</code>, <code>--applyExcludeFlags</code>) ===
=== Skip Records with any of the Specified Flags (<code>--buildExcludeFlags</code>, <code>--applyExcludeFlags</code>) ===
Use <code>--buildExcludeFlags</code> to skip records with any of the specified flags set when building the recalibration table, default 0x704.
Use <code>--buildExcludeFlags</code> to skip records with any of the specified flags set when building the recalibration table, default 0xF04.
By default, when building the recalibration table reads with any of the following flags set are skipped:
By default, when building the recalibration table reads with any of the following flags set are skipped:
* fails QC checks
* fails QC checks
* duplicate
* duplicate
* supplementary alignment
Use <code>--applyExcludeFlags</code> to skip records with any of the specified flags set when applying the recalibration table. The default value is 0x000, do not skip any reads.
Use <code>--applyExcludeFlags</code> to skip records with any of the specified flags set when applying the recalibration table. The default value is 0x000, do not skip any reads.
= Return Value =
= Return Value =
