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Published 20 hours ago • verified publisher icon nanoporetech

possibility to call mixed bases ?

Open alantsangmb opened this issue 1 year ago • 1 comments

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

alantsangmb avatar Jul 28 '22 03:07 alantsangmb

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.

cjw85 avatar Aug 10 '22 10:08 cjw85