Modern genomics workflows often require multiple specialized tools working in concert. In the upcoming VarSeq release, we are excited to announce the option for tighter integration with IGV. Genomics researchers and clinicians are well-versed in using IGV as a visualization tool for their genomic data. This new option will allow for synchronizing the view in the Golden Helix GenomeBrowser with IGV. This will make it easier to keep IGV in sync with the current variant or region selected in VarSeq.

Turning It On

Users of VarSeq will find the option to enable this feature in the options menu of the GenomeBrowser view. The option to change the port allows for the specification of which IGV instance to send the request to.

Please ensure that the port number selected in the GenomeBrowse options matches the port number selected in the IGV [View] => [Preferences] => Advanced section.

How It Works

Each running IGV instance has the option to listen on a port for commands. When enabled, you can send web requests to this port, which will update IGV (by default, IGV uses port 60151). VarSeq can now send updates to this location with the current location, keeping the two views in sync. All one has to do is select a variant, CNV, or region in VarSeq, and the IGV zoom will update when the GenomeBrowse zoom updates.

This allows users to combine VarSeq’s advanced filtering and visualization capabilities with the visual workflows they are familiar with in IGV. This will streamline validation and confirmation of variants coming through the analysis pipeline.

Lowering the Difficulty of Multi-Tool Workflows

Genomics researchers and clinicians regularly switch between different tools when deep diving into novel variants. With VarSeq and VSWarehouse 3 as the central hub of the analysis workflow this integration will help highlight the strengths that these tools have to offer, and cut out the tedious copy and paste workflows of the past. If you are interested in setting this up and trying it out in the new VSWarehouse 3 or VarSeq 3 releases please don’t hesitate to contact our team at [email protected].