Circular View

This page describes the integration of IGV desktop with the IGV-JBrowse CircularView 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, paired and split-read alignments from BAM/CRAM files, and arcs from bedPE and interact tracks.

Quick Start

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

   • Mac IGV JBrowse CircularView-0.1.1.dmg
   • Windows IGV JBrowse CircularView Setup 0.1.1.exe
   • Linux
     • IGV JBrowse CircularView-0.1.1.AppImage Note: must chmod+x after downloading.

2. Start IGV, open preferences (View > Preferences > Advanced tab), and insure "Enable port" is checked. For IGV versions <= 2.14.1 also insure that "Enable Circview" is checked. This option is located at the bottom of the Advanced preferences page.

3. Start the IGV JBrowse CircularView app.

4. In IGV, load one of the supported file types(see below). Features can be added to the circular view from the right-click 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.

   • 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.

5. In the circular view, click on chords to display both ends 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"