Duplicate Marking Implementation

Reads may be duplicated during sequencing, either due to clonal duplication via PCR before sequencing, or due to optical duplication while on the sequencer. To identify duplicated reads, we apply a heuristic algorithm that looks at read fragments that have a consistent mapping signature. First, we bucket together reads that are from the same sequenced fragment by grouping reads together on the basis of read name and read group. Per read bucket, we then identify the 5’ mapping positions of the primarily aligned reads. We mark as duplicates all read pairs that have the same pair alignment locations, and all unpaired reads that map to the same sites. Only the highest scoring read/read pair is kept, where the score is the sum of all quality scores in the read that are greater than 15.