Closed szhan closed 1 year ago
It turns out that MMR is not simply rho / mu. The relationship is more complicated, and it is explained a bit in #20. I did an experiment where I set mutation rate to 1e-8
and 1e-7
and ran the matching using MMR using the right formula. I then compared the imputed alleles from the experiments. I obtained more paths that are identical (in terms of the number of parent node ids correct) then simply maintaining rho / mu. There are, however, still some discrepancies, which may be due to numerical instability.
Right now, small values of
1e-8
and1e-20
are used for mismatch and switch probabilities, respectively. A previous preliminary analysis shows that precision set to get HMM path likelihood values can affect results (going from10
to20
, noticeably). So, even the set values of mismatch and switch probabilities may have an effect. It would be good to check by setting the mismatch and switch probabilities to, say,1e-6
and1e-18
, respectively, or possibly higher. It should be quick to test it on a handful of sample genomes anyway.