> 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/dragen-dna-pipeline/cnv-overview.md).

# Copy Number Variant Calling

The DRAGEN Copy Number Variant (CNV) Pipeline detects copy number aberrations and regions with loss of heterozygosity (LOH) from next-generation sequencing (NGS) data. It supports germline and somatic workflows for both whole-genome sequencing (WGS) and whole-exome sequencing (WES) in a single interface via the DRAGEN Host Software.

## Choose Your Workflow

Use the table below to identify the right pipeline for your use case and jump directly to its documentation.

| Sample type | Data type | Input samples  | Documentation                                                                                                    |
| ----------- | --------- | -------------- | ---------------------------------------------------------------------------------------------------------------- |
| Germline    | WGS / WES | Single / Multi | [Germline CNV Calling](/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview/cnv-germline.md) |
| Somatic     | WGS / WES | Single         | [Somatic CNV Calling](/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview/cnv-somatic.md)   |

Example commandlines are provided under [DRAGEN Recipes](https://github.com/illumina-swi/dragen-docs/blob/release/4.5-prod/product-guides/dragen-v4.5/user-guide/dragen-recipes/README.md).

Visit [Reference](/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview/cnv-reference.md) for more details on the CNV component.

## Before You Begin

Before running the CNV pipeline, ensure the following prerequisites are in place:

1. **CNV-enabled reference hashtable** — The hashtable must be built with `--ht-build-cnv-hashtable true`. This generates an additional k-mer uniqueness map used to correct mappability biases.
2. **Aligned BAM or CRAM input** — The pipeline accepts pre-aligned reads. If you are starting from FASTQ, first run map/align or use streaming alignments.
3. **Panel of normals (required for WES)** — WES normalization requires a panel of normals. WGS can use self-normalization instead.

## Pipeline Overview

The DRAGEN CNV Pipeline processes the input signal through the following stages:

**1. Target Counts** — Read counts and other signals are extracted from alignments and binned into target intervals.

![](https://25033470-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FG9szlFZupV6Q2DasL98y%2Fuploads%2Fgit-blob-b9f011edb411777e8603fb4dbccfdedc4ca191b9%2Fcnv-calling.SignalTargetCounts.png?alt=media)

**2. Normalization** — The case sample is normalized against a panel of normals or against the estimated normal ploidy. Systematic biases (e.g., GC bias) are corrected to amplify event-level signals.

![](https://25033470-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FG9szlFZupV6Q2DasL98y%2Fuploads%2Fgit-blob-1ed9998ea6b8062f6cdafa88458df5c92e6f3f5c%2Fcnv-calling.SignalNormalized.png?alt=media)

**3. Segmentation** — The normalized signal is segmented using one of the available segmentation algorithms.

![](https://25033470-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FG9szlFZupV6Q2DasL98y%2Fuploads%2Fgit-blob-f303c4ee46d0b8ca21974200f6093f32f00416b7%2Fcnv-calling.SignalSegments.png?alt=media)

**4. CNV Calling** — Events are called from the segments, scored, and emitted in the output VCF.

![](https://25033470-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FG9szlFZupV6Q2DasL98y%2Fuploads%2Fgit-blob-c7fe7ecefe956cb573102a5f97104328284c4ec9%2Fcnv-calling.SignalCalledEvents.png?alt=media)


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/cnv-overview.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.