Exclude Interval Files

To improve accuracy, the DRAGEN CNV Pipeline excludes genomic intervals if one or more the target intervals failed at least one quality requirement. The excluded intervals are reported to *.excluded_intervals.bed.gz file. The file identifies the regions of the genome that are not callable for CNV analysis and describes the reason intervals were excluded in the fourth column. The following are the possible reasons for exclusion.

Exclusion Reason	Description	Command Line Option
NON_KMER_UNIQUE	Nonunique Kmer bases are larger than 50% of interval.	Not applicable. This reason only applies to self-normalization mode.
BLACKLIST	Interval overlaps with blacklist larger than threshold.	--cnv-blacklist-min-overlap
PON_MAX_PERCENT_ZERO_SAMPLES	Number of PON samples with 0 coverage is larger than threshold.	--cnv-max-percent-zero-targets
PON_TARGET_FACTOR_THRESHOLD	Median coverage of interval is lower than threshold of overall median coverage.	--cnv-target-factor-threshold
PON_MISSING_INTERVAL	Target interval not found in PON	Not applicable.