New in Version 4.0.0

This version adds the following features, outlined below. Please note that pVACtools 4.0 is not backwards-compatible and certain changes will break old workflows.

Breaking Changes

  • pVACseq|pVACfuse|pVACbind report files have been reformatted to add some additional information and, in the case of pVACfuse and pVACbind, remove columns where all values were NA. Existing output files will no longer work with the standalone commands as well as pVACview.

  • The format of the Mutation Position column has been updated to no longer use 0 and n+1 to denote mutations starting before or ending after the epitope. This column now only shows the actually mutated positions.

New Features

  • We now support MHCflurry and NetMHCpanEL elution algorithms.

  • Users are now able to select specific amino acids that would be problematic for vaccine manufacturing and have the pipelines mark epitopes with such amino acids.

  • When running the reference proteome similarity step, users are now able to specify a peptide fasta to search against instead of using BLAST. Any exact matches against the entries in the peptide fasta are counted as a hit.

  • The aggregate report now takes into account many command line thresholds when tiering candidates. We also refined the way we determine the Best Peptide to take into account the biotype and TSL of the transcripts coding for the peptide, and whether or not the candidate has any problematic positions or fails the anchor criteria. Please see the output file section of the documentation for more details.

  • pVACview has been updated with a host of new features

    • Users may adjust a wider variety of thresholds for retiering.

    • Users are now able to reset the tiering thresholds to the ones originally used when running pVACview.

    • Transcripts resulting in the same set of epitope candidates are now grouped together to make it easier to identify unique candidates.

    • Elution data is displayed in the epitope details section of pVACview.

    • Reference match details are displayed in the transcript set details section of pVACview.

  • pVACfuse now supports output files from Arriba for fusion peptide predictions.

  • Users may provide an optional STAR-fusion output file to their pVACfuse run in order to extract expression and read support data for their candidates. These will be used for filtering, as well as for tiering in the aggregate report. Please see the output file section of the documention for more details.

  • When running the pvacseq generate_protein_fasta command, users are now able to specify an aggregated report as the --input-tsv. When using such a TSV, they can also use the --aggregate-report-evaluation to specify Evaluation statuses to include in the protein fasta. This is useful when creating a peptide fasta for vaccine ordering after using pVACview to select vaccine candidates and exporting the results to a new TSV.

Minor Changes

  • The reference proteome step is now run on the aggregated report instead of the filtered report.

  • A new parameter --aggregate-inclusion-binding-threshold controls which epitope candidates are included in the aggregate report.