What tools to use to generate these "chromothripsis" plot?

Question

[orangutan]

Hi,

I see this type of plot in many structural rearrangement papers, especially in cancer with a highly shattered genome ("chromothripsis" ). I have WGS data and have run a few tools to detect structural rearrangement. How can I visualize them in a similar way?

Answer 1

[Jonathan]

Hi, Shatter Seek (written in R) is a chromothripsis detection program that will generate similar plots to this, showing chromothripsis rearrangements. The program takes in two files with 1.) copy number data and 2.) structural variant data. You can customize the input format so the program is relatively agnostic regarding how you obtained the CN and SV files. The tutorial.pdf on the GitHub is pretty good.

https://github.com/parklab/ShatterSeek