> For the complete documentation index, see [llms.txt](https://help.bioinsight.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.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool.md).

# Variant visualization tool

The **Variant visualization tool** in **Emedgene** is based on the [Integrative Genomics Viewer (IGV)](http://software.broadinstitute.org/software/igv/home). It provides a high-resolution, interactive genomic view for validating and interpreting variant calls. Use the tool to review sequencing alignments, population data, functional predictions, curated annotations, and other supporting evidence in genomic context.

The **Variant visualization tool** supports SNVs, indels, MNVs, CNVs, STRs, and variants called with DRAGEN MRJD caller or DRAGEN Targeted caller. In v100.41 and later, it also supports translocations (TRA), inversions (INV), and breakends (BND).

## v100.41+

In v100.41 and newer:

* The **Variant visualization tool** is accessible from the [**Visualization tab**](/emedgene/emedgene-analyze-manual/variant_page/visualization_section.md) on the **Variant page** and from the [**Analysis tools tab**](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+.md) in **New mode**.
* The improved [**Track Manager**](/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/track-manager/track-manager-v100.40.0+.md) lets you control which [tracks](/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visualization-tracks.md) are displayed and their order, and reset your track order to your organization's default.
* More visualization tracks are available.
* You can open the **Variant visualization tool** in a [popup window](/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/open-the-visualization-tool-in-a-popup-window-v100.40.0+.md).
* [STR alignment visualization](/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/str-visualization-v100.41+.md) is available.
* Translocations (TRA), inversions (INV), and breakends (BND) are supported. See [**Default tracks**](/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visualization-tracks/default-tracks.md).

## v100.40+

In v100.40 and newer:

* The **Variant visualization tool** is accessible from the [**Visualization tab**](/emedgene/emedgene-analyze-manual/variant_page/visualization_section.md) on the **Variant page** and from the [**Analysis tools tab**](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+.md) in **New mode**.
* The improved [**Track Manager**](/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/track-manager/track-manager-v100.40.0+.md) lets you control which [tracks](/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visualization-tracks.md) are displayed and their order, and reset your track order to your organization's default.
* More visualization tracks are available.
* You can open the **Variant visualization tool** in a [popup window](/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/open-the-visualization-tool-in-a-popup-window-v100.40.0+.md).

## v100.39

In v100.39:

* The **Variant visualization tool** is accessible from the [**Visualization tab**](/emedgene/emedgene-analyze-manual/variant_page/visualization_section.md) on the **Variant page** and from the [**Analysis tools tab**](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+.md) in **New mode**.
* [**Track Manager**](/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/track-manager/viewing-modes.md) lets you control which [tracks](/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visualization-tracks.md) are displayed, individually and by category.

## v100.38

In v100.38:

* The **Variant visualization tool** is accessible from the [**Visualization tab**](/emedgene/emedgene-analyze-manual/variant_page/visualization_section.md) on the **Variant page**.
* [**Track Manager**](/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/track-manager/viewing-modes.md) lets you control which [tracks](/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visualization-tracks.md) are displayed, individually and by category.

## Learn more

<table data-view="cards"><thead><tr><th></th><th></th><th></th></tr></thead><tbody><tr><td><strong>Popup visualization window (v100.40+)</strong></td><td>Open the <strong>Variant visualization tool</strong> in a separate popup window for flexible review, including multi-monitor workflows.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/open-the-visualization-tool-in-a-popup-window-v100.40.0+.md">Learn more</a></td></tr><tr><td><strong>Track Manager</strong></td><td>Control which visualization tracks display in the <strong>Variant visualization tool.</strong></td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/track-manager.md">Learn more</a></td></tr><tr><td><strong>Visualization tracks</strong></td><td>Reference, curated, knowledge base, population, and optional signal tracks that add context to variant review in the <strong>Variant visualization tool</strong>.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visualization-tracks.md">Learn more</a></td></tr><tr><td><strong>Visual aids</strong></td><td>Variant highlighting overlays and reference lines that improve readability across tracks in the <strong>Variant visualization tool</strong>.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/visual-aids.md">Learn more</a></td></tr><tr><td><strong>STR visualization</strong></td><td>Open STR graph alignment images to inspect repeat structures and read alignments for STR variants.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/str-visualization-v100.41+.md">Learn more</a></td></tr><tr><td><strong>Adding variants to a case from the Variant visualization tool</strong></td><td>Add a variant to a case directly from the <strong>Variant visualization tool</strong> using coordinates from the current view.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> <a href="/emedgene/emedgene-analyze-manual/variant-visualization/variant-visualization-tool/manually-add-variant-from-igv.md">Learn more</a></td></tr><tr><td><strong>Variant visualization</strong></td><td>Review alignment, annotation, and population data in genomic context.</td><td><i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> Learn more</td></tr></tbody></table>


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