Circular View

This page describes integration of IGV desktop with the IGV-JBrowse Circular View application, a wrapper around the JBrowse 2 circular view component, for exploring structural variants and other long-distance interactions. Currently this integration supports structural variants from VCF files, and paired and split-read alignments from BAM/CRAM files. Support for bedPE and interact tracks is coming soon.

Quick Start

1. Download and install the IGV JBrowse CircularView app for your platform

   • 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 Note: must chmod+x after downloading.
     • igv-jbrowse-circularview-0.1.0.x86_64.rpm
     • igv-jbrowse-circularview_0.1.0_amd64.deb

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

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

   • 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 Pairs to Circular View - Add chords to the circular view for all features in view.

   • Alignment tracks (BAM and CRAM)

     • Add Discordant Pairs to Circular View - Add chords representing pairs separated by > 10 KB, or on separate chromosomes.

     • Add Split Reads to Circular View - Add chords representing split reads.

4. Clicking on chords in the circular view displays both ends of chords in IGV split screen mode.

Examples

SKBR3 cell line

Data courtesy of the Schatz Lab. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of the SKBR3 breast cancer cell line, Nattestad et al. (2017) Genome Research doi: 10.1101/gr.231100.117.

PacBio long read analysis

1. Start IGV

2. Start Circular View app

3. Verify the Circular View is enabled in View > Preferences > Advanced tab.

4. Load the following session from the menu item File > Load from URL. Note this is an unusually large and deep coverage long read file and initial loading can take up to 20 seconds.

https://raw.githubusercontent.com/igvteam/igv/master/test/sessions/circview/schatz_skbr3_longreads.xml

5. Right click over the "Sniffles variants" track and select "Add SVs to Circular View"

6. Click "Clear All" from the Circular View app

7. From IGV jump to gene "NEMF". (type NEMF in the IGV locus / search box and click "Go").

8. Right click over alignments and select "Add Split Reads to Circular View". You should now see arcs representing split reads from the region of NEMF in the circular view.

9. Click on one of the arcs to chromosome 17 to see both regions in IGV.

10. Right click over the reads for the rightmost panel (chr 17 region) and select "Add Split Reads to Circular View"

Illumina analysis

1. Start IGV

2. Start Circular View app

3. Verify the Circular View is enabled in View > Preferences > Advanced tab.

4. Load the following session from the menu item File > Load from URL.

https://raw.githubusercontent.com/igvteam/igv/master/test/sessions/circview/schatz_paired-end.xml

5. Jump to gene "NEMF". (type NEMF in the locus / search box and click "Go").

6. Right click over the "Delly SVs" track and select "Add SVs to Circular View".

7. Click on the arcs to chromosome 17 to see both regions in IGV.

8. Right click over the reads for the rightmost panel (chr 17 region) and select "Add Discordant Pairs to Circular View"