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nanoporetech / medaka

Sequence correction provided by ONT Research
https://nanoporetech.com
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possibility to call mixed bases ? #383

Closed alantsangmb closed 1 year ago

alantsangmb commented 2 years ago

Hello, I am trying medaka implemented in wf-artic to do CoV WGS. Just wondering whether medaka could call mixed bases when a minor variant exceed a certain frequency threshold? For example, a 'Y' can be called in the consensus sequences when both C and T are detected. Thank you

cjw85 commented 2 years ago

Hi @alantsangmb,

I don't think it likely that this feature be implemented. At its heard medaka is a consensus caller, not a variant caller -- it is not setup to provide indications of mixed populations of bases at a locus.