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