Fig. 2

Tumor-only mutation counts with filtering. a Boxplot showing numbers of mutations detected in the TGS cohort using tumor-only methods after each filtering step (left) and using matched tumor-normal methods on 182 sample pairs (right). b Boxplot showing numbers of mutations detected in the WES cohort using tumor-only methods after each filtering step (left) and using matched tumor-normal methods (right). c Boxplot demonstrating that in the TGS cohort, analyzing the normal samples independent of the tumor samples results in reduced ability to remove potential artifacts. GATK variant detection on all tumor and normal samples together, followed by isolation of the normal subset to annotate the tumor samples, results in the removal of more potential artifacts. Median counts are indicated by the dark line in the middle of the box. The bottom and top of the box are the first and third quartiles, respectively. The whiskers represent the most extreme points within 1.5 times the interquartile range. The y-axes are in a log scale