> For the complete documentation index, see [llms.txt](https://help.dragen.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.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/germline/standard-sbs/copy_number_variation_accuracy.md).

# WGS Copy Number Variation

Generated on **2026-05-13**

## Copy Number Variation

The DRAGEN Copy Number Variant (CNV) Pipeline can call CNV events using next-generation sequencing (NGS) data. This pipeline supports multiple applications in a single interface via the DRAGEN Host Software, including processing of whole-genome sequencing (WGS) data and whole-exome sequencing (WES) data. For more information, refer to the [DRAGEN user guide for germline CNV calling](/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview/cnv-germline.md).

**DRAGEN**: DRAGEN 4.5.4 | **Truthset**: HG002 NIST CNV v0.6 | **Reference**: GRCh38

<details>

<summary>Standard WGS CNV table (click to expand)</summary>

| Subtype   | Recall | Precision | F1-score |
| --------- | ------ | --------- | -------- |
| 1kb-10kb  | 0.968  | 0.977     | 0.973    |
| 10kb-50kb | 0.950  | 0.952     | 0.951    |
| >50kb     | 1.000  | 1.000     | 1.000    |

</details>

![CNV for Standard WGS](https://25033470-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FG9szlFZupV6Q2DasL98y%2Fuploads%2Fgit-blob-0b9cc561caf572379956ff49c60bb310bdea75b8%2Fcnv_accuracy_wgs.png?alt=media)

### Cytogenomics Modality

Conventional cytogenomics methodologies typically focus on larger alterations than the ones provided by NGS analyses. The Cytogenomics modality for the CNV caller allows the user to visualize variants at different resolutions, aiming at providing a more flexible workspace for different use cases. For more information, refer to [DRAGEN manual](/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview/cnv-germline.md#cytogenomics-modality).

<details>

<summary>Cytogenomics CNV summary table (click to expand)</summary>

| Group        | TP  | FN | Recall |
| ------------ | --- | -- | ------ |
| DEL 25kb-1Mb | 15  | 1  | 0.938  |
| DEL >=1Mb    | 46  | 1  | 0.979  |
| DUP 50kb-1Mb | 10  | 0  | 1.000  |
| DUP >=1Mb    | 29  | 1  | 0.967  |
| AOH >=500kb  | 43  | 0  | 1.000  |
| TOTAL        | 143 | 3  | 0.979  |

</details>

![Cytogenomics CNV Recall by Group](https://25033470-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FG9szlFZupV6Q2DasL98y%2Fuploads%2Fgit-blob-6ad1101a084913304c53a1452eacd31490dd3b29%2Fcytogenetics_cnv_recall.png?alt=media)


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