I tried sciClone (pubmedID 25102416) and having encountered some issues I'd appreciate hearing some thoughts on these.
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?
2. The program seems to have filtered away mutations with depth<100. Is it possible to decrease this limit?
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 output them?
Thanks in advance.