# 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+.

{% hint style="info" %}
**Note:** For CNVs, the overall [quality classification](/emedgene/emedgene-analyze-manual/variant_page/quality_section/variant-quality-summary.md) 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.
{% endhint %}

### Norm. depth of cov.

* Normalized depth of coverage, calculated by the [Ploidy caller](https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-dna-pipeline/ploidy-calling/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](https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-dna-pipeline/cnv-calling/additional-documentation/cnv-ascn) 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

{% hint style="info" %}
All metrics for CNVs and LOH/ROH called by array pipeline require DRAGEN Array 1.3+.
{% endhint %}

### 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.


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