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hdng / clonevol

Inferring and visualizing clonal evolution in multi-sample cancer sequencing
GNU General Public License v3.0
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PyClone-vi output #47

Open DrBlanco-Heredia opened 3 years ago

DrBlanco-Heredia commented 3 years ago

Dear Dr Dang,

The new version of PyClone (VI) gives the same CCF value in all variants sharing the same cluster per sample. Quoting the author of PyClone: "This is expected. The CCF quoted is the mean value of the cluster the mutation is assigned to. This differs from PyClone where we compute the mean value of the CCF across the MCMC samples. The latter better represents uncertainty over clustering, but I suspect it makes little difference in practice." This makes the box plots flat looking, since there's no variation inside clusters per sample (PDF attached). I believe this is not an issue for ClonEvol since the "infer.clonal.models" function takes precisely the mean value. I just want to be sure of it.

Thank you very much for your time and for this amazing tool. Box_4Mets.pdf

jsha129 commented 1 year ago

Dear developers, thanks for making this tool. I have a similar question to this one. pyclone-vi is much faster than pyclone. However, pyclone-vi only gives one CCF value for each clone. I assume pyclone would report CNA-corrected VAF for each mutation. Does the use of pyclone-vi change the results? Thanks