RegTools: Integrated analysis of genomic and transcriptomic data for discovery of splicing variants in cancer

The interpretation of variants in cancer is frequently focused on direct protein coding alterations. However, this analysis strategy excludes somatic mutations in non-coding regions of the genome and even exonic mutations may have unidentified non-coding consequences. Here we present RegTools, a software package designed to integrate analysis of somatic variant calls from genomic data with splice junctions extracted from transcriptomic data in order to efficiently identify variants that may cause aberrant splicing in tumors. RegTools is open source (MIT license) and freely available as source code or as a Docker image (http://regtools.org/).