Inter-chromosome translocations in short read WGS

Question

[German.M.Demidov]

Dear community members,

I feel quite comfortable with structural variants calling in WGS (human rare disease) except between-chromosome translocations. I use Manta for calling and I normally have tens to hundreds of "translocations" per sample.

How can I understand if a translocation is real?

I know that some of them are recurrent and thus anything that occur in a known region deserves a second look, but what about non-recurrent ones?

[cmdcolin]

We have worked on a tool for visualizing translocations in JBrowse 2. It may help you to understand your data https://jbrowse.org

I should get an example screenshot for short end reads but it works for paired end reads long split-reads too https://jbrowse.org/jb2/assets/images/breakpoint_split_view-fcc0006767af5061bedd51b05f95634f.png this tool is called the "breakpoint split view"

Not all translocations look this pretty, but certainly, if it does look "clean" like this it may be a good indicator of a clean translocation

[cmdcolin]

for alternatives samplot can also do some stuff like this too https://github.com/ryanlayer/samplot/issues/154#issuecomment-1086885900