Fig. 2

Detailed flowchart of the SCONCE2 pipeline. We demonstrate the pipeline with cell triplet \(\{A,B,C\}\), without loss of generality. Each tumor cell is initially independently analyzed through SCONCE, which gives parameter estimates and copy number profiles for each cell (red box). These parameter estimates are then summarized (yellow box), and branch lengths for tree \({\mathcal {T}} = \left[ t_1, t_2, t_3 \right]\) are estimated for each pair of cells (green box). Finally, for each cell, paired copy number profiles are summarized into a consensus copy number profile (blue box). Each step is fully described in Detailed SCONCE2 pipeline