What we're solving
IGV (Integrative Genomics Viewer) is an interactive tool for visually exploring genomic files. Terra users can open and view BAM, CRAM, and VCF files in workspace data tables in IGV (learn more).
Users have shared feedback that IGV in Terra lacks support for a common use case: 1) viewing files accessed via DRS URLs.
What's changing for you
For our first enhancement, the IGV integration in Terra now supports CRAM, BAM, and VCF files accessed using DRS URLs.
Benefits to your experience
Previously, users working with data hosted in NIH repositories (NHGRI AnVIL, NHLBI BioData Catalyst , NCI, etc.) or Terra Data Repository, could not automatically load DRS files into IGV -- they were required to download the file to their cloud storage bucket first. This was time-consuming and costly.
Now, IGV accepts the DRS URL directly for the sample of interest and its associated index file, which allows the tool to quickly stream the selected genomic coordinates (no need to download!).
We plan to iteratively roll out improvements to IGV -- check back often! We would also love to hear about your experience and any other improvements you would like to see.
Try it out
- Go to your workspace that has DRS URLs for genomic data.
- Find a data table row with DRS URLs for the sample of interest. The row must have both the primary file and its index in the same row. Currently, VCF, CRAM, and BAM files are supported.
- Click "Open With..." in the data table.
- Click "IGV".
- (Note that "Searching for valid files with indices..." briefly appears)
- After waiting a few seconds, click the checkbox for your sample.
- Click "Launch IGV".
- Note you see a track for your sample.
- In the IGV search box, type in a coordinate or gene of interest (For example, for a VCF type "LDLR", then press "Enter" / "return" on your keyboard).
- Explore your sample in IGV!