> For the complete documentation index, see [llms.txt](https://docs.omics.ai/products/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.omics.ai/products/workbench/variant-interpreter/reviewing-variants/genome-browser.md).

# The genome browser (IGV)

Every variant has a **Browser** view — an embedded IGV genome browser centered on the variant. Use it to inspect the underlying evidence directly: see the aligned reads, judge call quality, and place the variant in its genomic context alongside genes and other annotation tracks.

## What you see by default

The browser opens at the variant's locus with the tracks relevant to the variant type already loaded. Every variant gets:

* a **Reads** track: the sample's read alignments, grouped and coloured by haplotype;
* a **Current Variant** track marking the variant you opened;
* gene models (**Genes (RefSeq)** and **MANE v1.0 - RefSeq**).

The other default tracks depend on the variant type:

| Variant type        | Additional default tracks                                                                                                 |
| ------------------- | ------------------------------------------------------------------------------------------------------------------------- |
| Small variants      | ClinVar SNVs, AbSplice Scores, dbSNP 155 Common, dbSNP 155 ClinVar, HPRC Variants <= 3bp, PhastCons 30-way, PhyloP 30-way |
| Structural variants | ClinVar CNVs, CADD 1.7 Deletions, AbSplice Scores, dbSNP 155 ClinVar, CpG Islands                                         |
| Copy number         | CpG Islands, ClinVar CNVs, CADD 1.7 Deletions, CADD 1.7 Insertions                                                        |
| Tandem repeats      | PanelApp STRs, CpG Islands, RepeatMasker                                                                                  |

The browser is genome-aware: the tracks available to add depend on the reference genome the analysis was run against.

{% hint style="info" %}
For a methylation region, the browser instead loads each available family member's reads as a separate **Haplotagged Reads** track (for example, **Proband — Haplotagged Reads**), grouped by haplotype. When more than one member is available, a checkbox per member (**Proband**, **Father**, **Mother**, …) above the browser shows or hides that member's track. The browser doesn't show separate methylation signal tracks; see [Methylation & imprinting](/products/workbench/variant-interpreter/reviewing-variants/methylation-imprinting.md).
{% endhint %}

## Opening the browser

Open the **Browser** tab in the variant drawer. You can also jump straight to it from:

* **Open in IGV** on a structural variant's **Read Support** card. This opens the browser on the junction, showing both breakpoints. See [Structural variant detail](/products/workbench/variant-interpreter/reviewing-variants/structural-variants/structural-variant-detail.md).
* **Verify in the genome browser** on the **Haplotype phase** panel, when a pair of variants can't be placed in cis or trans. See [Haplotype phase (cis/trans)](/products/workbench/variant-interpreter/reviewing-variants/haplotype-phase.md).

{% hint style="warning" %}
For very large structural variants, the browser opens on a 2 Mb window centred on the middle of the event rather than the whole span. Pan or zoom out to reach the far breakpoints.
{% endhint %}

## Adding and removing tracks

Open the **track selection** dialog to change what's displayed. It offers three ways to add data:

* **Track hubs** — curated hubs of reference tracks, organized into categories and groups (for example, gene predictions or regulatory annotations). Browse a hub and pick the tracks you want.
* **Hub tracks** — individual tracks from an already-loaded hub, toggled on or off.
* **Load from URL** — point the browser at your own track file by URL (with an optional index), for data not in a hub.

Tracks you add appear immediately; remove them from the same dialog to declutter the view.

## Working in the browser

Standard IGV navigation applies — pan, zoom, and jump to a locus. The browser is scoped to the sample and analysis you have open, so what you see reflects exactly the data behind the variant you're interpreting. Use it to confirm a call before you classify it: check read depth and allele balance, look for strand bias, and see whether nearby variants share the same reads.


---

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