Keep only reads whose mate maps to the same contig or is unmapped
Category Read Filters
Overview
Keep only reads that have a mate that maps to the same contig (RNEXT is "="), is single ended (not 0x1) or has an unmapped mate (0x8).See MappedReadFilter for criteria defining an unmapped read.
Additional references
See these additional references.
GATK version 4.1.3.0 built at Sat, 23 Nov 2019 16:20:54 -0500.
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