how to highlight hotspot rearrangments regions?

Question

[vmicrobio]

Hello biostars community

I would like to understand what happened in a human genome containing some complex rearrangements. I would like first to focus on a/some region/s containing potentially rearrangements and then look deep at the hybrid reads present in this particular region. However there are potentially several big regions.

I'm looking for suggestions or specific tools to highlight hotspots regions with hybrid reads.

Thanks a lot!

Answer 1

[vmicrobio]

It seems that the best way is to try different SV callers and compare results. I found an interesting comparative list of softs (Guan and Sung, Methods, 2016) : [1]https://ibb.co/Zhky3Hn