Fig 3. Inter-caller agreement.

Pairwise comparisons of the nine studied variant callers in exome sequencing of five breast cancer samples in exome sequencing and deep sequencing data in upper and lower panels, respectively. The matrix depicts the agreement among the studied variant callers. In each horizontal line, the number reflects the fraction of calls found by the caller that are also reported by the other callers. For instance, looking at EBCall in the first line, Mutect reports 51% of the calls reported by EBCall. Deep sequencing data includes only data covered by 200 x at minimum in both tumor and normal sample. The color reflects the degree of agreement, with the highest color intensity depicting high agreement between the two callers.