MateOnSameContigOrNoMappedMateReadFilter

Keep only reads whose mate maps to the same contig or is unmapped

Category Read Filters

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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.

• MappedReadFilter

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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.