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 4.0.3

We added an optional downstream analysis tool to generate an annotated fasta file from a VCF with protein sequences of mutations and matching wildtypes. This tool can be run with the pvacseq generate_protein_fasta command.

This release fixes a couple of errors that were introduced in the previous version which would occur during the processing of certain inframe indels.

This version also fixes an error that would occur if the number of variants to process was a multiple of the chosen --fasta-size.


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.