picard picard UmiAwareMarkDuplicatesWithMateCigar

picard UmiAwareMarkDuplicatesWithMateCigar

Identifier: TL_e24fa5_0b.c8


Identifies duplicate reads using information from read positions and UMIs. This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. It is based on the MarkDuplicatesWithMateCigar tool, with added logic to leverage Unique Molecular Identifier (UMI) information. In addition to assuming that all members of a duplicate set must have the same start and end position, it imposes that they must also have sufficiently similar UMIs. In this context, 'sufficiently similar' is parameterized by the command line argument MAX_EDIT_DISTANCE_TO_JOIN, which sets the edit distance between UMIs that will be considered to be part of the same original molecule. This logic allows for sequencing errors in UMIs. This tool is NOT intended to be used on data without UMIs; for marking duplicates in non-UMI data, see MarkDuplicates or MarkDuplicatesWithMateCigar. Mixed data (where some reads have UMIs and others do not) is not supported.


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