pVAC-Seq has been renamed to pVACseq and is now part of the pVACtools immunotherapy tools suite. The pvacseq package will no longer be updated or maintained. Please update your local installation to the pvactools package. Please see the pVACtools documentation for more information.

pVAC-Seq is a cancer immunotherapy pipeline for the identification of personalized Variant Antigens by Cancer Sequencing (pVAC-Seq) that integrates tumor mutation and expression data (DNA- and RNA-Seq). It enables cancer immunotherapy research by using massively parallel sequence data to predicting tumor-specific mutant peptides (neoantigens) that can elicit anti-tumor T cell immunity. It is being used in studies of checkpoint therapy response and to identify targets for cancer vaccines and adoptive T cell therapies. For more general information, see the manuscript published in Genome Medicine.

New in version 4.0.10

This is a hotfix release to fix a bug with how certain types of frameshift mutations were handled. Previously, we were not creating the correct mutant peptide sequence for these variants. See this GitHub issue for more information.

This version also includes a sanity check to error out if the wildtype amino acid in the wildtype protein sequence differs from the expected wildtype amino acid as listed in the protein change. This situation might occur if the VCF was annotated with a different reference build than the one used for alignment and variant calling.


Jasreet Hundal, Beatriz M. Carreno, Allegra A. Petti, Gerald P. Linette, Obi L. Griffith, Elaine R. Mardis, and Malachi Griffith. pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens. Genome Medicine. 2016, 8:11, DOI: 10.1186/s13073-016-0264-5. PMID: 26825632.


This project is licensed under NPOSL-3.0.