It would be relatively easy to save the intermediate tree sequence just before the first Delta sample, then re-run the initial part of the Delta matching (perhaps restricting sample matching to only Delta samples and those samples ancestral to the Delta samples in Fig S8).
I think running just this part of the matching should be very quick, and repeated application of this part of the analysis might allow us to work out which combination of HMM parameters, site exclusions, etc work well to remove this particular false positive, and the impact any changes might have on related recombination nodes. I imagine this could be worked up in to some sort of evaluation test.
It would be relatively easy to save the intermediate tree sequence just before the first Delta sample, then re-run the initial part of the Delta matching (perhaps restricting sample matching to only Delta samples and those samples ancestral to the Delta samples in Fig S8).
I think running just this part of the matching should be very quick, and repeated application of this part of the analysis might allow us to work out which combination of HMM parameters, site exclusions, etc work well to remove this particular false positive, and the impact any changes might have on related recombination nodes. I imagine this could be worked up in to some sort of evaluation test.