Supplementary Figure 4: Additional results from assessing cardelino and alternative methods using simulated data.

Assessment of cell assignment to clones across a variety of simulation settings, considering SingleCellGenotyper (SCG), Demuxlet, cardelino and its two versions: cardelino-free without any informative clone configuration prior and cardelino-fixed assuming that the clone configuration prior is correct (Methods; Supplementary Note). All methods were applied to simulated data with known ground truth, varying (a) the number of informative variants per clonal branch, (b) the fraction of informative variants covered (that is, nonzero scRNA-seq read coverage), (c) the total number of clones, (d) the precision (i.e., inverse variance) of allelic ratio across genes; lower precision means more genes with high allelic imbalance, (e) the rate of general errors of mutation states in the clone configuration matrix, (f) the fraction of wrongly clustered variants in the input clonal tree branch. Default parameter values are marked with an asterisk and are retained when varything other parameters. (g) The effects of the tree topology on the cell assignment accuracy. In the simulations there are 50 repeats for each parameter, where one of the tree topology candidates is randomly selected in each repeat. For the four-clone configurations, there are four different tree topologies (upper panel), and their performance (area under the precision-recall curve) for the five different methods are splitted (bottom panel).