As new somatic mutation callers are developed, the cancer genomics community will greatly benefit from a systematic performance measurement using the approaches described here across the entire parameter space of tumor and normal depths and mutation allele fraction. Our method as well as the tools we developed to benchmark mutation detection methods are available, and we encourage methods developers to report the characteristics of their method using these metrics. The approaches described here can also be extended to other alterations such as indels or rearrangements.
