Visualization tools for split read / structural variants

Question

[mikothebichon]

Hi everyone,

I have been trying to curate my SV call set by visually going through the bamsnap images (a static version of IGV) of each SV region. However, it is difficult to look at long-range information, such as the paired-end reads, or when a read is mapped to different regions, using this approach.

I am wondering if there exist tools that can: 1) show all the alignment with respect to the reference; 2) show the mapping of the split reads to reference; 3) extract pairs of discordant/clipped reads (not necessarily have to be the same tool).

I would also love to know how other people are curating SV call sets. Any advice would be greatly appreciated.

Answer 1

[cmdcolin]

We have been developing tools in JBrowse 2 to try to help view split reads across large SVs. One of these we call the "breakpoint split view", here showing long split reads connecting different chromosomes

See more here https://jbrowse.org/jb2/gallery/

We are definitely interested in getting more users and trying to make things easier. The desktop version was just released so you can download it as an app to your computer for easy use, with hg19 and hg38 preconfigured

Answer 2

[Pierre Lindenbaum]

I played with this problem by writing a few experimental tools.

for example SV2SVG generates a an animated SVG file showing were the supplementary reads map on two regions. http://lindenb.github.io/jvarkit/SvToSVG.html

see also: Visualizations of chimeric connections in different chromosomes