Background

This guide aims to assist Genomic Laboratory Hub (GLH) Clinical Scientists using the Integrative Genomics Viewer (IGV) to review data for Rare Disease and Cancer referrals in the Genomic Medicine Service (GMS).

GMS supports IGV as both a web application accessed on the Interpretation Portal and the download of batch scripts to run IGV locally.

This document covers:

1. How to access IGV through the Interpretation Portal
2. How to load relevant WGS files in both the IGV web application and IGV Desktop
3. A brief introduction to technical assessment of variants of interest

Getting started

Using IGV Visualising Rare Disease Visualising Cancer

Supporting or Reference Documents

For further assistance and information on the use of IGV for Cancer or Rare Disease variant visualisation, please refer to the IGV user guide or contact the Genomics England Service Desk.

Known Issue: Refresh Token Bug

We are aware of an issue on the IGV.js web application where the 'Refresh Token' button at the top of the screen is not working correctly. We are hoping to address this when we next update our IGV.js implementation, and would like to apologise for any issues it may be causing you.