If you look at the help (with ?sciClone), you'll find many of the answers you're looking for. 1. My copy number data used for input is log-ratio data. It seems though as sciClone interpreted it as absolute copy number data, since only cn=2 were used (and according to the paper, sciClone only looks at VAFs in regions of normal cn). Is it possible to make the program use the log-ratio data? When calling the sciClone() function, set cnCallsAreLog2=TRUE 2. The program seems to have filtered away mutations with depth<100. Is it possible to decrease this limit? SciClone works best with deep readcounts, as they decrease the uncertainty associated with each VAF. That said, if you want to decrease it, when calling the sciClone() function, change the minimumDepth parameter. 3. Finally, the output contains one cluster. However, visually there are 3 subclusters in that cluster. I understand they are too close to each other to be considered separate clusters. Is it possible to make the program... - Chris Miller