MetricsReadFilter

Filter out reads that fail platform quality checks, are unmapped and represent secondary/supplementary alignments

Category Read Filters

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Overview

Filter out reads that:

• Fail platform/vendor quality checks (0x200)
• Are unmapped (0x4)
• Represent secondary/supplementary alignments (0x100 or 0x800)

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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.