Duncan Mbuli-Robertson

To test the dating performance on singletons with new phase-agnostic algorithm, I used the 1500 individual subset I made of the 1kgp-chr20p data. That way, I could use the singletons...

Just remembered that I can't install from GitHub in GEL anymore, so I unfortunately can't test it until they approve the Airlock transfer of this branch of tsdate, annoyingly! I...

> Thanks @duncanMR, very helpful and a lot to chew on. > > > is the high proportion of variants with invalid posteriors also surprising to you? > > could...

> > it's the root-to-sample edges problem > > Oh -- I think I missed the discussion of this previously. What is going on? Are these not simply mutations that...

> @duncanMR two things that occurred to me -- we should be using mutation posteriors here; as that takes a weighted average of the two branch midpoints (posterior mean) rather...

When adding singletons in GeL that Sam extracted, there are sites where the alternative allele (e.g. A) is a singleton, but there is another alternate allele (e.g. T) at the...

@nspope Adding singletons is failing for chr17p in GEL. It's a bit annoying that it didn't show up in the 1kgp data, since I can't share a reproducible example. It...

> That is interesting. I can see the LD calculator causing problems as that does a lot of seeking backward and forward (was the original motivation for bidirectional seeking). I...