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yatisht / usher

Ultrafast Sample Placement on Existing Trees
MIT License
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Impute deletions as well as substitutions? #186

Open fritzo opened 2 years ago

fritzo commented 2 years ago

Thanks for building a great tool! I'd like to use UShER to impute mutations along a tree. I see the mut.mut_nuc proto field is repeated, so in theory deletions and even insertions are representable. However the SARS-CoV-2 mutation annotated tree has only substitutions, and indeed discussion in #179 suggests UShER treats deletions as missing data.

Is it totally out of scope to model deletions? Is there a workaround to try to impute deletions from a mutation-annotated tree? Should I be using a different tool instead?

yatisht commented 2 years ago

In a (distant) future version of UShER, we do plan to support insertions and deletions as well, but it's not happening soon, unfortunately. I am not aware of a different tool to help with this. @russcd, do you know of any?

-Yatish