Quick Start Part 4 Workspace gt Analysis

IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click here

created by Geraldine_VdAuwera

on 2018-01-07

The Integrative Genomics Viewer (IGV) is a powerful genome visualization tool that assists researchers in performing complex variant analysis. FireCloud has integrated igv.js, a mini version of IGV desktop with fewer features, to make it easy for you to preview your cloud stored genetic data right in your workspace without needing to download the whole file. However, if you need access to the more sophisticated features of IGV or use a reference other than HG 19, you will need to set up your desktop IGV application to connect to Google Cloud Storage. We plan to provide documentation to that effect in the near future.

Select Tracks

IGV displays data in horizontal rows called tracks. Check out the IGV User guide to learn how to interpret and navigate the browser. The file format inputs accepted are: BAM, VCF, and BED. Note: igv.js does not support CRAM viewing.

When you click “Select Tracks”, the data model will load so that you can select one or more files to view as individual tracks. Accepted files will display in the same order you clicked. You can sort the track viewing order here by dragging and dropping the tracks before loading.

Note that IGV requires an index file (“.bai”) to load a BAM successfully.

Load

At load time, the tracks will be zoomed out to view approximately 250 million base pairs at Chromosome 1 against a HG19 reference. You cannot view anything at this default setting, so you will have to zoom in or type in what locus or gene symbol you want to view. Mutation formats (KRAS:G12C or KRAS:123A>T) are not an accepted notation in the search field.

Updated on 2018-04-20