# Combine 5-base methylation and variant data

The *Combine 5-base methylation and variant data* task enables users to combine annotated differentially methylated regions (DMRs) and annotated variants, for dual-omics insights in DNA Methylation Prep data analysis.

## Running Combine 5-base methylation and variant data

The *Combine 5-base methylation and variant data* task expects annotated DMRs and annotated variants data within the same analysis. This task can be invoked at either *Annotated regions* data node or *Annotated variants* data node.

* Click **Annotated regions** or **Annotated variants** data node.
* Click **Combine multiomics data** section in the context-sensitive task menu.
* Click **Combine 5-base methylation and variant data**.
* Click **Select data node** to select another data node (*Annotated variants* or *Annotated regions*) for intersection or union.

<figure><img src="https://580316046-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWMxqQAMFOJtu98OBk9KN%2Fuploads%2Fgit-blob-7e15a93d90c60438786173e2e21a6deeb0cbd5c1%2F5base-variant-dialog.png?alt=media" alt=""><figcaption></figcaption></figure>

* Data nodes that are selectable for combine are in blue. In example below, *Annotated regions* data node from the methylation analysis branch are selected.

<figure><img src="https://580316046-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWMxqQAMFOJtu98OBk9KN%2Fuploads%2Fgit-blob-d3cc240481c4a74d2e54a08dacf4812022384074%2Fselect-node-for-dual-omics.png?alt=media" alt=""><figcaption></figcaption></figure>

* Select **intersection** or **union** to combine methylation and variant data, then click **Finish**.
  * Intersection: Use gene ID to intersect DMRs and variants. Every intersected variant and DMR will be reported in an individual row in task report.
  * Union: Report intersection (by gene ID) result and also variants that overlap DMR by specified distance (default is +/- 1000bp).

## Task output

When complete, double-click on **5-base methylation and variants** data node to open result. The task report is similar to the [Summarized cohort mutations](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/variant-analysis/summarize-cohort-mutations) task report, with an additional column **Origin** to indicate if result in a row is present in both methylation and variant data (VC, DMR), or variant data only (VC), or methylation data only (DMR).

<figure><img src="https://580316046-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWMxqQAMFOJtu98OBk9KN%2Fuploads%2Fgit-blob-fcb4f37e58c8cc95eee7384847f66be90680e8c2%2F5base_variant_intersect_report.png?alt=media" alt=""><figcaption></figcaption></figure>
