Mutation Detection Software for Bench Scientists

The accurate detection of bona fide causal DNA mutations in a sequenced sample is critical for gene function discovery studies. The rapid sequencing rate and high-throughput nature of next-generation sequencing (NGS) technologies have greatly accelerated the pace of discoveries in molecular genetics. The computational task of detecting DNA variants in large-scale NGS sequencing datasets may be daunting for the typical bench scientist. In an era of tremendous advances in computing and reliable cyberinfrastructure availability, empowering wet-lab scientists to independently perform computational analysis on sequencing datasets without the requirement for detailed knowledge of the underlying hardware and software infrastructure is a very desirable goal. We describe the initial implementation of a user-friendly DNA variant-detection software for the analysis of NGS sequencing datasets called Variant-Scope. Variant-Scope is implemented in Python and provides an intuitive user-interface (UI), and also includes a setup configuration wizard, computation status viewer, and a variety of summary charts and figures generated for an experimental study. Variant-Scope integrates cutting-edge NGS analysis software suites such as BWA (for reads alignment), SAMtools (for variant detection), BEDTools (for genome arithmetic), and SnpEff (for variant-effect annotation), and is distributed as a package for users running Windows, MacOS, or Linux. Variant-Scope is a very flexible package and can handle sequencing datasets ranging from whole-genome sequences of single individuals to large populations. The package is freely available and has been successfully utilized for the detection of both Fast-Neutron and EMS-induced DNA variants in a variety of mutagenized populations