How to access breakpoint split view in jbrowse 2

breakpoints.md

JBrowse 2 has a special "view type" called the "breakpoint split view" that allows you to see the connection between split long reads (e.g. SA tag) and paired-end reads

Ways to access the breakpoint split view

Using the SV inspector to launch a breakpoint split view

The SV inspector lets you load a VCF containing SV calls and then will launch a "breakpoint split view". Note that the breakpoint split view that it launches will be empty but you can then add your BAM or CRAM reads to it (on both top and bottom levels sometimes is needed)

Fig1. Clicking on a "chord" of the SV inspector

Fig2. Clicking on the dropdown menu of the SV inspector. Note that it gives the option for "top/bottom" and "single row"

Using the 'feature details' panel of a regular linear genome view to launch a breakpoint split view

Recent versions added the ability to launch th breakpoint split view directly from the "feature details" of an alignments feature or variant feature

Fig3. The feature details from clicking on a long read in a plain old linear genome view with links to "Launch split view". Note that it gives the option for "top/bottom" and "single row"

Fig4. The feature details from clicking on a variant call in a plain old linear genome view with links to "Launch split view". Note that it gives the option for "top/bottom" and "single row"

What is the difference between "top/bottom" and "single row"?

• The top/bottom "mode" of the breakpoint split view stracks two independent linear genome view vertically.
• The single row "mode" is split "left/right" in a single linear genome view