I have been using SciClone to check clonality changes between pre- and post- treatment tumor. It is an impressive tools and the figure generated seems reasonable and easy to interpret.
However, SciClone paper claims that it only makes clonality inference from variants' VAF within CN neutral region. Then why do I see clusters on non-CN neutral region (1 copy and 3 copies)? How are they inferred? Is it that SciClone only uses VAF within CN neutral region to establish the baseline and later infers clusters on non-CN neutral region after adjusting the VAF based on the ploidy?