> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/quality_section/quality-metrics-per-variant-type/cnv-quality-metrics.md).

# 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+.

{% 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 %}

### 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

{% 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.

### 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.


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