Viewing IGV tracks of BAM files

Allie Hajian
  • Updated

This article walks through two ways to use the Integrative Genomics Viewer (IGV) to examine tracks from BAM (.bam) files in Terra. The instructions assume that the BAM and BAM index files are in a data table. 

1. From the workspace Data page

You can link data files in the cloud to your workspace by including the file URL in a data table of your workspace. To view these files in IGV, follow the step-by-step instructions below.

1.1. Select a row from the table (the sample must include both a BAM and BAI file).
View-IGV-tracks_Select-samples-and-choose-edit_Screen_shot.png

1.2. Click the Open with icon above the table. 

1.3. Select IGV.
S26b_Jun21_2019.png

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

1.6. You can then navigate to the region of interest.
S26c_Jun21_2019.png

2. Using the IGV web app

You can also use IGV in a web browser following the steps the below. We recommend keeping your data page open in a separate browser tab, since you'll be copying and pasting links to the data files (i.e. URLs) from your Terra data table to the IGV browser.

2.1. Right click the BAM file link in the data table and select Copy Link Address.
S26g_Jun21_2019.png

 

2.2. Open IGV (http://igv.org/app/) in a new browser tab. 

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

2.4. Select Tracks > URL.

2.5. Paste the BAM file URL from the data table into the Data URL field. 
S26f_Jun21_2019.png

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

2.7. Paste the BAI URL into the Index URL field in IGV.

You should see the tracks in the web browser.
S26h_Jun21_2019.png

Save tracks to view later

You can save the tracks for viewing later using Share (from the top menu). 

Example 

See the example IGV web browser file created from this example at http://bit.ly/2IqsQqM.

 

 

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