Exclude BED Filtering

You can input an exclude BED to the CNV caller to filter out regions from analysis. Inputting an exclude bed is useful if there are certain regions in the genome that are known to be problematic due to library prep, sequencing, or mapping issues. You can also exclude larger intervals that specify common CNVs to aid in downstream analysis. You can create an exclude BED file using cnv-exclude-bed. DRAGEN does not provide an exclude BED. The intervals to exclude should be formatted in standard three-column BED format.

The intervals in the exclude BED are compared with the original target counts intervals. If the overlap is greater than cnv-exclude-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. The *.tn.tsv.gz files excludes the removed intervals.

An excluded 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 excluded interval. However, the call would not take read counts from excluded intervals into account. You can view explanations for excluded intervals in the *.excluded_intervals.bed.gz file.