Create a file containing the reads that mapped, but where the read pair did not meet the requirements to be considered an intact pair within the mapping. Reasons for failing to be considered an intact pair include:
- reads of the pair mapped with incorrect relative orientations
- reads of the pair mapped at a distance outside the expected range
- reads of the pair mapped to different reference sequences
- one of the two reads of the pair did not map to any of the references
Further details can be found in Options for All Programs.