I am trying to use Sciclone to do clustering on my paired diagnostic and relapsed WES data. However, all the clusters in each patient are around line y=x. But I expect to see some clusters like the cluster 4, 5 in the example figure, which was only in the diagnostic or only in the relapsed sample. How can I fix this?
example figure: Figure 3a
"Miller, Christopher A., Brian S. White, Nathan D. Dees, Malachi Griffith, John S. Welch, Obi L. Griffith, Ravi Vij et al. "SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution." PLoS computational biology 10, no. 8 (2014)."