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genome / sciclone

An R package for inferring the subclonal architecture of tumors
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Incorporating CNA events #22

Closed kippakers closed 8 years ago

kippakers commented 8 years ago

Hi, I'm curious if your suggested strategy for incorporating CNA variants into a clonality analysis has changed since the the Sciclone paper in 2014. I'm looking to assign clone numbers to mutations from tumor samples using sciclone but I don't want to exclude variants in CNA regions.

Is it reasonable to simply "adjust" a VAF directly by the copy number of that variant?
ie VAFnew = VAF/(CN/2)

chrisamiller commented 8 years ago

It's not as simple as just adjusting - here's an explanation of why: https://www.biostars.org/p/106774/#106834

At present, the strategy is still to exclude those regions. Other algorithms exist that try to assign these points, but I don't have enough experience with them to comment on their effectiveness at this time.

kippakers commented 8 years ago

Thanks for the info!