Additional information is generally required in order to reliably select the correct tumor purity and ploidy solution from the set of candidates identified by fitting the model in (4). In a given tumor sample, several combinations of theoretically possible purity, ploidy, and copy number values may map to equivalent copy ratios (Supplementary Fig. 1c,h). Furthermore, the presence of subclonal SCNAs may result in a spuriously high ploidy solution with an implausible karyotype receiving a greater SCNA-fit likelihood by over-discretizing the copy profile, allowing their assignment to integer copy-levels (Supplementary Fig. 1h-j).
