Duplicate Marking

DRAGEN RNA can detect duplicate reads, which are defined as fragments that have both ends mapping to the same (clipping-adjusted) position during alignment. In RNA data, the reads can represent PCR duplicates during library prep or as a result from deep coverage of highly expressed regions. If --enable-duplicate-marking is set to true, duplicate fragments are marked in the BAM file and the total number of duplicate reads is reported as a mapping metric. Marking of duplicates does not affect gene expression quantification and gene fusion calling.