feature request: option to mark optical duplicates only

[eboyden]

Hi - would it be possible to add an option to the duplicate marking function to only mark optical duplicates? Most PCR-free applications, including most WGS workflows, would benefit from this. Note that ideally there would also be a means to control the distance - other tools e.g. Picard typically use 100 for unpatterned flow cells and 2500 for patterned flow cells by default (although in the latter case this may be too low and marking by tile may be better).

Related: UMI-aware duplicate marking would also be appreciated, although I realize that this might be more complicated to implement.

[seboyden]

For PCR-free libraries, similar to Novosort, ideally there would be both an --opticalOnly option with a distance threshold for true optical duplicates on unpatterned flow cells, as well as a --pcrFree option to mark ExAmp duplicates on patterned flow cells, which would mark duplicates within the same flow cell lane or tile, since ExAmp duplicates travel much farther than optical duplicates.