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 field 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.

Copy Number

• Estimated number of copies in the region according to the VCF FORMAT CN field.

Allele-Specific Copy Numbers

• In addition to the total copy number, based on read depth, the platform can display minor and major allele copy numbers identified by the DRAGEN CNV ASCN module in the format [minor/major].
• Requires DRAGEN 4.4+.
• Available for WGS cases from version 100.39.0+.

CNV Quality Score

• Phred-scaled confidence score produced by the CNV caller.
• Higher values indicate greater confidence.
• Requires DRAGEN 4.3+.

Size

• CNV length in base pairs.
• Size value according to the SVLEN INFO field of the CNV variant.
• Requires DRAGEN 4.3+.

Bin Count

• Number of read-depth bins spanning the CNV.
• Bin count value according to the BC INFO field of the CNV variant.
• Requires DRAGEN 4.3+.

Mean LRR (Log R Ratio)

• Shows signal intensity balance across the CNV region.
• Calculated as log₂(NR).
• Mean LRR value according to the NR FORMAT field of the CNV/LOH variant.
• Values close to 0 suggest normal regions; large positive or negative values suggest gains or losses.
• Requires version 100.39.0+.

Mosaic Fraction

• Provides a mosaic fraction estimate for mosaic events.
• Mosaic fraction value according to the MF FORMAT field of the CNV/LOH variant.
• Requires version 100.39.0+.

Norm. depth of cov.

• Normalized depth of coverage according to the NDC FORMAT field, calculated by the DRAGEN Ploidy caller.
• Requires DRAGEN 4.2+ and version 100.39.0+.

Likelihood Ratio

• Measures confidence in the CNV call. A log₁₀ ratio of ALT versus REF probability.
• Likelihood ratio value according to the LR INFO field of the CNV variant.
• Higher values indicate stronger evidence.
• Available for exome and panel cases.
• Requires DRAGEN 4.3+.

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.

Copy Number

• Estimated number of copies in the region according to the VCF FORMAT CN field.

Mosaic Fraction

• Provides a mosaic fraction estimate for mosaic events.
• Mosaic fraction value according to the MF FORMAT field of the CNV/LOH variant.

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.

LRD

• Deviation from expected log ratios.
• Essential for identifying LOH/ROH and assessing call quality.