Filter out reads that fail platform quality checks, are unmapped and represent secondary/supplementary alignments
Category Read Filters
Overview
Filter out reads that:- Fail platform/vendor quality checks (0x200)
- Are unmapped (0x4)
- Represent secondary/supplementary alignments (0x100 or 0x800)
GATK version 4.1.1.0 built at Sat, 23 Nov 2019 17:29:19 -0500.
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