OpenVax: An Open-Source Computational Pipeline for Cancer Neoantigen Prediction

OpenVax is a computational workflow for identifying somatic variants, predicting neoantigens, and selecting the contents of personalized cancer vaccines. It is a Dockerized end-to-end pipeline that takes as input raw tumor/normal sequencing data. It is currently used in three clinical trials (NCT02721043, NCT03223103, and NCT03359239). In this chapter, we describe how to install and use OpenVax, as well as how to interpret the generated results.