Fig. 3

Allele Frequencies of Somatic and Germline Variants and Required Coverage for Somatic Variant Detection by Simulation. The top half of each graph shows the expected allele frequency of somatic (blue) and germline variants (red) by tumor content (x-axis) for different copy number states (plot titles, N indicates total copy number, M indicates minor allele copy number). The bottom half of each graphs shows the coverage required (indicated by the color) to get the power indicated by the y-label. Black squares indicate that the detection power was not achieved even at the highest coverage evaluated. We can see that the closer the somatic and germline allele frequencies, the more difficult it is to detect somatic variants