Nature Methods
Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection
Adam D Ewing, Kathleen E Houlahan, Yin Hu, Kyle Ellrott, Cristian Caloian, Takafumi N Yamaguchi, J Christopher Bare, Christine P'ng, Daryl Waggott, Veronica Y Sabelnykova, Michael R Kellen, Thea C Norman, David Haussler, Stephen H Friend, Gustavo Stolovitzky, Adam A Margolin, Joshua M Stuart, Paul C Boutros.
The first report of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge introduces the BAMSurgeon tool for accurate tumor simulation and reports the performance of 248 submissions in calling single-nucleotide variants from three pairs of synthetic tumor–normal genome benchmarks.