computing chromothripsis on cancer genomes

Question

[Bogdan]

Dear all,

please would you advise if there is any package that computes the areas with chromothripsis, given the cancer genome data (i.e. either the lists of CNV, or DEL, DUP, INV, or starting from BAM files) ? Thank you !

-- bogdan

[Thind amarinder]

Is it WES or WGS data?

Answer 1

[Jonathan]

I have recently started using Shatter Seek (written in R) for chromothripsis detection. 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

Answer 2

[d-cameron]

GRIDSS2/PURPLE/LINX (https://github.com/hartwigmedical/hmftools/tree/master/linx https://www.sciencedirect.com/science/article/pii/S2666979X22000325) is currently the most mature pipeline for performing complex rearrangement classification and interpretation.