Recognition of tumor neoantigens is a major factor in the activity of clinical immunotherapies \cite{25838375}. Therapeutic vaccines targeting neoantigens \cite{24777245} are showing promising results in clinical trials \cite{25837513}.
There are a few published pipelines for neoantigen identification \cite{26825632}, with accompanying open source software.
We'd like to improve the accuracy of neoantigen identification by comparing the performance and identifying the most informative stages of each pipeline.