FilterDuplicates plugin

Use the FilterDuplicates plugin to remove duplicate reads from merged data after a run is completed. The removed BAM files are saved in the FilterDuplicates directory. The original BAM files in the main analysis directory are not modified.

The Mark as Duplicate Reads feature in the main analysis pipeline marks reads as duplicates but does not remove them from the BAM files. Enable this feature in the Kits step of Planned Run creation.