HPexome: An automated tool for processing whole-exome sequencing data

Whole-exome sequencing has been widely used in clinical applications for the identification of the genetic causes of several diseases. HPexome is a command-line tool that automates many data processing tasks for exome-sequencing data analysis of large-scale cohorts. Given ready-analysis alignment files, HPexome breaks input data into smaller pieces defined by genomic regions and efficiently processes them in parallel using cluster-computing environments. It relies on the Queue workflow execution engine, GATK variant calling tool, and its best practices to output a high-confident multi-sample genomics variant file.