Fig 4. Comparison of subclone detection methods in 78 PCAWG samples with mean effective sequencing depth (purity * depth) of greater than 60x.

(A) Number of subclone estimates using different methods including MOBSTER [16], sciClone [24], and TumE. (B) Comparing agreement and disagreement between existing methods in the analyzed PCAWG samples. (C) Comparison of the estimated subclone frequency in PCAWG samples versus simulated data across different methods. Consistent with simulated data where each method properly identified the presence of 1 subclone, TumE consistently captures higher frequency subclones when compared to MOBSTER. (D–F) Visualization of the 3 samples where each TumE and MOBSTER detected 1 subclone. sciClone fits are provided for comparison. Single-nucleotide variants (SNV) with annotations in known driver genes [8,16] were labeled if present.