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 analysis already loaded — the sample's read alignments and gene models for the analysis's reference genome. The browser is genome-aware: the tracks available to add depend on the reference genome the analysis was run against.

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.