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 4.1.5.0-SNAPSHOT built at Wed, 4 Mar 2020 13:47:07 -0500.
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