This article explains two ways you can use the Integrative Genomics Viewer (IGV) to examine tracks from BAM (.bam) files in Terra.

1. From the workspace Data tab
2. From the IGV web app

1. From the workspace Data tab

Data files in the cloud linked to your workspace will appear in the data table of the Data tab of your workspace. To view these files in IGV, follow the step-by-step instructions below.

1.1. Select a row from the table that has both a BAM and BAM.bai file

1.2. Select the vertical three dot icon that appears next to the download button

1.3. Choose "Open with..."

1.4. Select IGV

1.5. Choose the appropriate reference for the files and select launch

1.6. Navigate to the region of interest

2. Using the IGV web app

You can also use IGV in a web browser using the steps the below. You'll be copying and pasting file links from your Terra data table to the IGV browser, so we recommend keeping your Terra Data page open in a separate tab.

2.1. In Terra, right click the file name for the BAM file you want to view and select Copy Link Address

2.2. In a new web browser tab, navigate to the IGV Browser at http://igv.org/app/

2.3. Select "Genome" and choose the appropriate reference genome

2.4. Select "Tracks" --> "URL"

2.5. Paste the BAM file location you copied from your data table into the DATA URL

2.6. Copy the BAI (index file) path from the Terra data table as you did for the BAM in Step 2.1.

2.7. Paste the BAI link to the BAI file in IGV Index URL section

The tracks are now viewable in the web browser.

You can save the tracks for viewing later by pressing "Share" at the top menu. 

To see the example IGV web browser file created from this example, go to this URL: http://bit.ly/2IqsQqM.