Msprime: Planned feature: gene conversion

[jeromekelleher]

Gene conversion is important if we are to simulate bacterial populations. We plan on adding gene conversion following the methods in Brown et al 2016.

There is a complication in that we will not be able to support gene conversion exactly on a non-uniform recombination map. We will need to clearly state this limitation.

[russcd]

This would be totally fabulous/useful feature! Please let me know when it's been added and I'll be more than happy to give the beta a spin.

[jeromekelleher]

Thanks @russcd, we'll try and schedule this for implementation soon. There is a bit of a backlog of stuff to get through I'm afraid though, so it'll be a while...

[russcd]

No worries. Thanks so much for all your hard work!

On Mon, Oct 3, 2016 at 12:42 AM, Jerome Kelleher [email protected]
wrote:

Thanks @russcd https://github.com/russcd, we'll try and schedule this
for implementation soon. There is a bit of a backlog of stuff to get
through I'm afraid though, so it'll be a while...

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[jeromekelleher]

Unfortunately it's looking unlikely that I'm going to have the time to implement this any time soon. It's a pity as it's an important feature which would be widely useful I think, but realistically I just have too many other things to implement now.

However, I'd be very happy to work with someone who wanted to implement gene conversion in msprime. I have a pretty clear picture of how it would be done, and I don't think it's a huge amount of work. Please contact me offline if anyone would like to discuss.

[jeanrjc]

Hello,

I'd be interested in having such a feature as well.
Are there any news on its development ?

Best
Jean

[jeromekelleher]

Hi @jeanrjc. Hopefully @fbaumdicker and I will be working on this over the coming months and will report here when we have something that is useable.

[jgallowa07]

Any news on this, @jeromekelleher ?

[jeromekelleher]

Any news on this, @jeromekelleher ?

Batting this one over to @fbaumdicker!

[fbaumdicker]

Any news on this, @jeromekelleher ?

Batting this one over to @fbaumdicker!

I am definitely on it. This is currently WIP. The python version should be ready within this month and the C version within this year. However, it seems there is more demand for this feature than expected, so maybe I should reschedule some other projects to realize this faster?
@jgallowa07 If you are interested in testing the python version, let me know.

[jeromekelleher]

If you get the Python version working well @fbaumdicker, I'm happy to help with the C stuff and I'm sure we'd get it sorted pretty quickly. There's a lot of interest in this feature.

[andrewkern]

i'm also willing to lend a hand at this. I'm interested in it myself and have implemented the coalescent with gene conversion before.

[jeromekelleher]

If you open up a PR on the Python prototype with what you have @fbaumdicker, we can probably move forward pretty quickly.

[fbaumdicker]

Ok! Great to have you all on board. I will prioritize this and open up a PR as soon as possible.

[jgallowa07]

May not have any time for implementation, but happy to do some beta testing!

[hyanwong]

@fbaumdicker I would love to have GC in msprime for a student project too, so here's another vote for prioritising. I'm also happy to do some beta testing.

[fbaumdicker]

I opened the PR for gene conversion python prototype #781
Everyone is welcome to do some beta testing.
There is certainly more effort necessary to speed up the simulation by using further Fenwick trees and or splitting up the two currently used rates (gene conversion within and left of individuals) into three processes (gene conversion within segments left of first segments and between segments).

[jeromekelleher]

Closing this as the project is well under way and covered by other issues.