Our First App — Broad’s IGV

We’re excited to announce our first app — the Broad’s Integrative Genomics Viewer (IGV). IGV brings the power of a rich genome browser to your BaseSpace data. It also shows you what launching apps will be like in BaseSpace.

BaseSpace Data in IGV

IGV is a fully featured genome browser that allows you to visualize your sequence data in great detail. It is a desktop application that can load data both from your local computer and over the Internet. We’ve modified IGV to display alignment and variant data from BaseSpace (BAM and VCF files). This allows you to perform variant analysis after launching Resequencing or Amplicon workflows in BaseSpace.

Launching the IGV App in BaseSpace

Launching IGV from BaseSpace is simple. After selecting IGV from the App Launcher, you’ll be asked for permission to allow IGV to read your BaseSpace data. Then IGV launches (your browser downloads a ‘jnlp’ file – in some browsers you may need to manually open this file). Launching IGV in BaseSpace is also context sensitive. When you’re viewing an analyzed Sample in BaseSpace and you launch IGV, the Sample will be highlighted in IGV. Currently, you can launch IGV in BaseSpace from the Sample Details page of an App Result.

Browsing BaseSpace Files in IGV

When you launch IGV, you’ll give the app permission to view everything in one of your Projects. We’ve added a file explorer to IGV so you can navigate your Project’s data within IGV. Only BAM and VCF files will show for now (i.e. alignments and variants). Just double click to load them into the browser (it’s best to load variants — the VCF files —  first to they don’t get hidden below an alignment track).

How did we develop the IGV app?

We developed the IGV app just as any developer will develop apps for BaseSpace. That is, we used the BaseSpace API to access BaseSpace data. We’ve released our version of the IGV app as open source on github – check it out to see how we used the API and add features if you wish. If you want to create your own apps with the BaseSpace API, check out our developer portal.

We hope you find the IGV app useful for analyzing your BaseSpace data. Let us know what you think! We’re excited to release IGV as our first app. Check back here for announcements about more apps to come.

About Eric Smith

Eric Smith is a product owner for BaseSpace.

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