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, 01:07, 6 March 2016
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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. |
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| 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: |
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| * fails QC checks | | * fails QC checks |
| * duplicate | | * duplicate |
| + | * supplementary alignment |
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| 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. |
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− | These parameters were added in version 1.0.10.
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| = Return Value = | | = Return Value = |