Circular View

This page describes integration with the IGV electron wrapper of the JBrowse Circular View component. The wrapper provides 2-way communication between IGV and the circular view for exploring structural variants and other long-distance interactions. The view works with VCFs encoding structural variants, bedPE and "interact" tracks, and paired end and split-read alignments.

1. Download and install the IGV JBrowse CircularView app

• MacOS IGV JBrowse CircularView-0.1.0.dmg
• Windows IGV JBrowse CircularView Setup 0.1.0.exe
• Linux IGV JBrowse CircularView-0.1.0.AppImage

2. Install the development snapshot version of IGV

3. Start IGV, open preferences ("View > Preferences > Advanced tab), and check "Enable circview"

4. Load one of the supported file types (see below). Features can be added to the circular view from the track menus as follows.

   • Variant tracks (VCF): "Add SVs to Circular View": Adds chords to the circular view for all variants in view that have info fields "CHR2" and "END". These fields are commonly added by Structural Variant callers.

   • Interact tracks (BEDPE and INTERACT): "Add features to Circular View": Add chords to the circular view for all features in view.

   • Alignment tracks (BAM and CRAM) Two menu items, "Add discordant pairs to Circular View" and "Add split reads to Circular View"