IGV Visualizations

Connected Insights includes an embedded Integrative Genomics Viewer (IGV) that can be used to view sequencing reads and evaluate variant quality.

1. To display the variant in IGV, select the IGV button in the Biomarker Details for variants.

2. To display the date in IGV, perform one of the following actions:

   • To view data at the variant level, select the IGV column entry for the variant.

   • To view data at the case level, select Case Visualization above the grid. The IGV visualization is displayed in a new browser tab.

3. To display the data for a local file, select Local File, and then navigate to an IGV-formatted file.

4. To display the genome sequence data, select UCSC Genome Browser.

   ❗ Large visualization files must be compressed before upload.

5. To view reference tracks, select IGV Track Settings, and then select the checkboxes for the tracks or group of tracks you want to view.

6. [Optional] View break ends. The breakend view zooms in on the ends of the breakpoints in the sequence.

   • To visualize breakends in separate views, select View Breakends.

   • To return to a single breakend view, select Join Breakends.

7. [Optional] Select Add New Comment to add or update a comment about the variant. Each new or updated IGV comment is copied as a separate entry to the Variant Details tab comments for the variant.

   ❗ The Variant Details tab does not indicate the source of the comments. To differentiate entries created in IGV, preface comments with IGV or another short identifier.

8. Use the following options to interact with the visualization:

   • Zoom into an area of interest.

   • Pan the visualization by clicking and dragging or by selecting the left and right arrows on the karyogram.

   • Select an item in the visualization to view additional information about the item.

   • Show or hide IGV elements.

     • Karyotype Panel

     • Track Labels

     • Center Line

     • Cursor Guide

   • Change the track settings.

     • Set track name.

     • Set track height.

     • Collapse, squish, or expand exon rows.

     • Remove track.

   ❗ The gene model display track reflects the transcript reference standard (Ensembl or RefSeq) specified in Settings.