visualizing more complex rearrangement events

[rbuels]

The breakpoint split view is a good first step, but we need more powerful tools to understand more complex rearrangement events.

Figure idea: https://www.nature.com/articles/s41586-019-1913-9/figures/3 Tool that makes similar figures: http://mskilab.com/gGraph/

A paper with more crazy rearrangement stuff: https://www.biorxiv.org/content/10.1101/2020.10.15.340497v1.full.pdf

[cmdcolin]

to me, the "possible derived chromosome" is one of the best part of the figures....being able to correctly get the derived chromosome and even get things like a gene track mapped over to that would be amazing, and is something I think will become bigger along with "assembly based SV calling"

[rbuels]

i.e. use synteny style views to look at the rearranged genome vs the reference, and see genes and other annotations mapped to it, or at least on the other side of the synteny relationship

[rbuels]

Needs more brainstorming.