The indel-calling step was performed by the Genome Analysis Toolkit SomaticIndel Detector with default parameters. The highly confident indels were identified by an in-house pipeline and further annotated as germline or somatic on the basis of whether any evidence of the event at the same locus was observed in the normal data. Finally, highly confident SNVs were annotated with ANNOVAR and used in follow-up analysis. A full list of mutation events is presented in Table S3.