Keep only reads with mates mapped on the different strand
Category Read Filters
OverviewFor paired reads (0x1), keep only reads that are mapped, have a mate that is mapped (read is not 0x8), and both the read and its mate are on different strands (when read is 0x20, it is not 0x10), as is the typical case.
See MappedReadFilter for criteria defining an mapped read.
See these additional references.
GATK version 126.96.36.199 built at 02-49-2019 01:49:44.