Detecting Somatic Insertions/Deletions (Indels) Using Tumor RNA-Seq Data

Identification of somatic indels remains a major challenge in cancer genomic analysis and is rarely attempted for tumor-only RNA-Seq due to the lack of matching normal data and the complexity of read alignment, which involves mapping of both splice junctions and indels. In this chapter, we introduce RNAIndel, a software tool designed for identifying somatic coding indels using tumor-only RNA-Seq. RNAIndel performs indel realignment and employs a machine learning model to estimate the probability of a coding indel being somatic, germline, or artifact. Its high accuracy has been validated in RNA-Seq generated from multiple tumor types.