How to distinguish subclone from sciClone or PyClone result

Question

[bioxujintian]

Hello everyone,

I used sciClone and PyClone to cluster mutations, but don't konw how to distinguish founding clone and subclone. I would really appreciate if someone could answer this question.

[bioxujintian]

Thanks, Miller. Do you mean the highest VAF cluster in a sample is the founding clone in this sample?

[Chris Miller]

Usually that is the case

Answer 1

[Chris Miller]

The founding clone is made up of the set of mutations that is in every cell of the tumor. It generally corresponds to the highest-VAF clone (which should be highest in all samples)