Add chromothripsis #32
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…variations() in simulate_endToEnd.py
…simulate_endToEnd.py
…ons in tests/test_simulate_endToEnd.py
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Well, it looks like this passes. I'm still skeptical, but...
If so, then this branch should create chromothripsis. One reserves entire chromosomes to be rearranged with SVs (except no insertions).
One then creates no more SVs in these chromosomes---users will know there could be issues with the coordinate system.
In this case, I would be interested in creating an log file only for "chromothriptic rearrangements" for each chromosome, possibly using our existing infrastructure and
import logging. Talk to Nick about this. I suspect it's straightforward to do---log the events in the order they take place, and allow users to "work backwards" if they are so inclined.reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065307/
Based on Stephens et al 2011, it looks like chromothripsis happening on 20-200Kb. I believe this is the current length scale, but users could crank this up/down via the probability parameter.