Blacklist Filtering

You can input blacklist BED to the CNV caller to filter out regions from analysis. This is useful if there are certain regions in the genome, which are known to be problematic. You can also blacklist larger intervals that specify common CNVs to aid in downstream analysis. DRAGEN does not provide a prebuilt blacklist, but you can use the cnv-blacklist-bed option to specify the intervals to blacklist. The intervals should be formatted in standard three-column BED format.

The intervals in the blacklist are compared with the original target counts intervals. If the overlap is greater than cnv-blacklist-min-overlap, the target counts interval are excluded from analysis. The *.target.counts.gz file still includes the interval, so you can inspect the original read counts. The normalization stage removes intervals and is reflected in the *.tn.tsv.gz file.

A blacklist interval does not guarantee that a CNV call does not span the interval. If there is sufficient data flanking the region, the segmentation stage along with any merging might still generate a call spanning the blacklisted interval. However, the call would not take read counts from blacklisted intervals into account.