Correct recombination probabilities #404
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hyanwong
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I have now updated this to bound both the recombination probabilities and mismatch probabilities at 0.5, as discussed in #403 (comment). For our own reference, I have written a reasonably extensive discussion of the parameterisations & meaning of the arrays in the docstrings of the This should fix #398 |
tsinfer/inference.py
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| ``recombination`` probabilities measure the probability of a recombination event | ||
| between adjacent inference sites, used to calculate the HMM transition probabilities | ||
| in the L&S-like matching algorithm. When matching a haplotype against the ancestor | ||
| in the immediately previous generation, ``recombination`` probabilities should reach |
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"generation" is a bit misleading here - we don't have any concept of time and I think this will confuse people. A recombination proba of > 0.5 is always a weird thing, for example when dealing with LD calculations. This is a pretty standard issue when thinking about these extreme values for probability values in mutation and recombination processes. I think we can just say something like "Note that values > 0.5 for the recombination and mutation parameters will likely lead to pathological behaviour - for example, a mismatch probability of 1 means that a mismatch is required at every site.".
But nailing these parameters down as probabilities is very valuable and a great clarification!
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Yep. I suspect they are actually likelihoods (because they are conditional on a hypothesis, that this is the actual hidden state), but since everyone calls them probabilities, I guess we might as well stick with that.
Great. Do we want an assert (perhaps only in the python version of the algorithm) that we have only 2 alleles, so that we don't forget we need to change the emission probs for > 2? |
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I'll follow up with something to take care of that (#415) |
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This is a template for the sort of thing I suggest we might use to fix #398 . It still suffers from pathological probabilities with extreme values of e.g. mismatch_ratio, though. Some of this might need to be discussed in conjunction with #403