# LocusZoom DNAnexus App

The LocusZoom app visualizes GWAS result files stored on the DNAnexus Platform including an interactive Manhattan plot, QQ plot, and a table of high p-value loci, as well as standard LocusZoom regional plots. It supports the use of GRCh37 and GRCh38 reference genomes.

This DNAnexus app is based on the [hosted LocusZoom](https://github.com/statgen/locuszoom-hosted) codebase and uses a virtual machine, so it incurs compute charges during use. The GWAS results stay on the DNAnexus Platform while using this app.

The LocusZoom app is launched from the **Tools Library** menu as shown below:

![](https://1612471957-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-L_EsL_ie8XyZlLe_yf9%2Fuploads%2Fgit-blob-25776f59520887b6a347d19f134d76a287be1e24%2FLocusZoomStart.png?alt=media)

A user can specify an array of GWAS results files to visualize as the app's input. These files show up in the GWAS file dropdown once the app is running. You can also visualize other GWAS results by entering file IDs of a platform file with the GWAS results in the input entry field.

![](https://1612471957-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-L_EsL_ie8XyZlLe_yf9%2Fuploads%2Fgit-blob-32e3b9eb63a6b8071c1aadfbfd1545dbc7485bfc%2FLocusZoomFileDropdown.png?alt=media)

After selecting which GWAS results file you want to view, a set of interactive dialogs that recognize common GWAS results formats appear on screen. You can select more specific settings for the GWAS visualization, and select **Next** when you are done.

![](https://1612471957-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-L_EsL_ie8XyZlLe_yf9%2Fuploads%2Fgit-blob-934822e9842a40bff17195419c63838b5a28bc0e%2FLocusZoom%20file%20sniffer.png?alt=media)

{% hint style="info" %}
The **Analyze** tab displays the file in "Pending" state during import and changes to "Ready to View" state when the GWAS results are ready to visualize.
{% endhint %}

![](https://1612471957-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-L_EsL_ie8XyZlLe_yf9%2Fuploads%2Fgit-blob-0f10fe02ddcf5f9592817cce56bf45cc3e2fabcf%2Flz_ready.png?alt=media)

Once your file is done loading, clicking on the name of the file in the **Analyze** tab brings up the LocusZoom interactive analysis environment.

![](https://1612471957-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-L_EsL_ie8XyZlLe_yf9%2Fuploads%2Fgit-blob-446510926c3fd05ff67585fb1e0cc86da37de16f%2FLocusZoom-analyse.png?alt=media)

Clicking on a locus on the Manhattan Plot or in the Top Loci table zooms into the locus:

![](https://1612471957-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-L_EsL_ie8XyZlLe_yf9%2Fuploads%2Fgit-blob-fcae1df062f38482bc3e7f91d29cbd3901c97c78%2Flz1.png?alt=media)

This app does not save its state. Follow the steps above to re-import the GWAS results file in another instance of the LocusZoom app if you want to view the visualization again.


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