Fig. 3.

Accuracy of mutation clustering by ddClone, OncoNEM and B-SCITE for 100 simulated clonal trees with 10 nodes (clones) and 50 mutations. For the single-cell data, we drew 25 genotypes from each clonal tree for various values of parameter λ, which controls bias in sampling single cells from clones (large values of λ indicate a small bias, where the probability of drawing a single cell from a given clone is usually close to its prevalence in the entire tumour cell population). We also added the following noise to the single-cell genotypes: false-positive rate 10⁻⁵, false-negative rate 0.2, missing (NA) rate 0.05 and doublet rates 0, 0.1 and 0.2. Bulk data coverage was set to 10,000, and variant read counts drawn from a binomial distribution. We obtained data sets from trees for each parameter combination. A more detailed description of the simulation data is given in Supplementary Methods. For the definition of V-measure see ref. ³⁶. Source data are provided as a Source Data file