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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 cellular_prevalence or just VAF for clonevol #3

Closed crazyhottommy closed 7 years ago

crazyhottommy commented 7 years ago

Hi, I have finished pyclone, and want to use clonevol for downstream analysis. Should I just the cellular_prevalence or just VAF for clonevol?

Thanks! Tommy

hdng commented 7 years ago

If your variants include ones in CN-altered region, you should take the CCF and divide by 2, to get "copy number adjusted VAF", and use that in clonevol. Otherwise, either way is fine.

crazyhottommy commented 7 years ago

Thanks! I will use the cellular_prevalence/2.

immuneAI commented 1 year ago

Hi @crazyhottommy Could you explain or example of your code you used in using clonevol with pyclone output, this would be a great help.