CNV quality metrics

The following metrics are calculated for CNVs depending on the caller and assay type.

CNVs called by NGS pipeline

VCF Filter

• The FILTER column value in the VCF, indicating whether a variant passed the caller's quality thresholds or failed specific checks.

• Requires DRAGEN 4.3+.

Note: For CNVs, the overall quality classification is not determined solely by the VCF FILTER value.

CNVs can be assigned HIGH quality based on CNV-specific criteria (such as SVCLAIM=DJ), even if they do not have a PASS filter in the VCF.

Norm. depth of cov.

• Normalized depth of coverage, calculated by the Ploidy caller.

• Requires DRAGEN 4.2+ and version 100.39.0+.

Copy Number

• Estimated number of copies in the region.

Allele-Specific Copy Number (ASCN)

• In addition to the total copy number, based on read depth, the platform can display minor and major allele copy numbers identified by the CNV ASCN module in the format [minor/major].

• Requires DRAGEN 4.4+. Available for WGS cases.

CNV Quality Score

• Phred-scaled confidence score produced by the CNV caller.

• Higher values indicate greater confidence.

Size

• CNV length in base pairs.

Bin Count

• Number of read-depth bins spanning the CNV.

NR

• Requires DRAGEN Array V1.2+ and version 37.0+.

LRD

• Requires DRAGEN Array V1.2+ and version 37.0+.

Likelihood Ratio

• Measures confidence in the CNV call.

• Higher values indicate stronger evidence.

• Requires DRAGEN Array V1.3+ and version 100.39.0+.

Mean LRR (Log R Ratio)

• Shows signal intensity balance across the CNV region.

• Calculated as log₂(NR).

• Values close to 0 suggest normal regions; large positive or negative values suggest gains or losses.

• Requires DRAGEN Array V1.3+ and version 100.39.0+.

Mosaic Fraction

• Provides a mosaic fraction estimate for mosaic events.

• Requires DRAGEN Array V1.3+ and version 100.39.0+.

Likelihood Ratio Score (LRS)

• A log₁₀ ratio of ALT versus REF probability.

• Requires DRAGEN 4.3+. Available for exome and panel cases.

CNVs and LOH/ROH called by array pipeline

All metrics for CNVs and LOH/ROH called by array pipeline require DRAGEN Array 1.3+.

VCF Filter

• Indicates whether the variant passed DRAGEN quality checks.

Likelihood Ratio

• Measures confidence in the CNV call.

• Higher values indicate stronger evidence.

Mean LRR (Log R Ratio)

• Calculated as log₂(NR).

• Shows signal intensity balance across the CNV region.

• Values close to 0 suggest normal regions.

• Large positive or negative values suggest gains or losses.

Mosaic Fraction

• Provides a mosaic fraction estimate for mosaic events.

CNV Quality

• Shows the caller’s overall confidence in the variant.

Size

• CNV length in base pairs.

Bin Count

• Shows how many data bins (probe regions) support the CNV.

• A higher bin count means stronger support for the CNV.