Keep only reads with mates mapped on the different strand

Category Read Filters


For 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.

Additional references

See these additional references.

Return to top

See also General Documentation | Tool Docs Index Tool Docs Index | Support Forum

GATK version built at 10-58-2018 11:58:10.