Keep only reads whose mate maps to the same contig or is unmapped
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.
See these additional references.
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GATK version 220.127.116.11 built at 09-43-2018 09:43:10.