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.