How to Get Started Using IGV

Learn how to install and configure The Integrative Genomics Viewer (IGV) from The Broad Institute to explore genomic information from Kannapedia Reports.

Download and Install IGV Software

To get started with this feature, one must first download the IGV software.  For convenience, here are the recommended download links for MacOS, Windows, and Linux.  If you visit the Download page directly, it is recommended to download and install the Java Included version of the software for the appropriate operating system on your computer.

Important note: Once IGV is downloaded, it’s important to have the software open and running before you attempt to make use of the IGV integration on Kannapedia.  Here is how to get started:

1. Open IGV 

You will probably see something like this - IGV may come loaded up with Human as the default reference.  This is perfect - IGV is up and running so leave it open and don’t close it.

Explore Variants on

Navigate to a Kannapedia report with variants.  Here is one if you aren’t sure where to go to.

Click the IGV "Start" link for one of the variants in the table

The orange arrow above shows where the Start link is for the variant p.Arg534His (a coding change in the protein at amino acid 534 that results in a change from Arginine to Histidine in the CBCAS gene). Note there is also a blue arrow pointing to a "Jump" link.  Click the Start link to get started - and make sure the IGV software is already open as described in Step 1.

Important note: You must first click the "Start" link each time you visit a new Kannapedia report. After that, you can use the "Jump" link to more quickly navigate to other areas of interest. 

Important note:  If you visit a new page for a new sample, make sure to hit Start again or else Jump links will take you to the variant for the sample you were previously looking at and not the current sample.

Here is what you should see after you click on the Start link in the example for p.Arg534His:

Zoom out to view the full gene 

To illustrate what is in here, it may be more useful to zoom out (using the “+/-” buttons in the top right corner).  When we zoom out a bit, here is what we see:

Tracks included in the IGV

Different tracks are presented in this example.  Since it is an NGS-based report, there are two additional tracks showing coverage and sequencing reads that are not present for a CannSNP90 derived sample.  The tracks are as follows (from top to bottom):

  1. Variants (VCF file)
  2. Coverage
  3. Sequencing Reads (BAM file)
  4. Gene Annotation

An in-depth review of all the features of IGV is beyond the scope of this document but refer to this instructional video from Medicinal Genomics to see more as well as several tutorials provided by The Broad Institute here as well as a User Guide.