Keep only reads whose mate maps to the same contig or is unmapped
Category Read Filters
OverviewKeep 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.
See these additional references.
GATK version 18.104.22.168 built at Thu, 5 Dec 2019 09:51:56 -0500.