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removing fixed mutations

See original GitHub issue

We can at times end up with a large number of fixed mutations. It would be nice to have a way to remove these. I think we discussed having simplify() do this, but it does not:

ts = msprime.simulate(10, recombination_rate=2, mutation_rate=2)
sts = ts.simplify([0,1])
sts.genotype_matrix()
### 
array([[1, 1],
       [1, 1],
       [1, 1],
       [1, 0],
       [1, 1],
       [1, 1],
       [1, 1],
       [1, 1]], dtype=uint8)

This would require a bit of bookkeeping (e.g. updating the ancestral state at sites that still have a segregating mutation). Not sure whether to propose this as an argument to simplify (filter_fixed_mutations) or as its own function. This is not urgent, as far as I know, but if we were to change the default behavior of simplify, it would be nice to do it soon.

Issue Analytics

State:
Created 4 years ago
Comments:22 (22 by maintainers)

Top GitHub Comments

1reaction

jeromekellehercommented, Jul 15, 2019

Ah, I see. Should we add a filter_fixed_simple_sites (or something) option to simplify then? I think catching the single mutation fixed sites is pretty easy? I don’t want to call it monomorphic or whatever as I think this is misleading in the multiple mutation case.

0reactions

petrelharpcommented, Jun 25, 2022

You did, and it was tricky, but it’s probably a good bit easier now - we’ve got more tools.

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