griffithlab/pVACtools: 6.0.0

What's Changed

This is a major version release. Please note that pVACtools 6.0 is not guaranteed to be backwards-compatible and certain changes could break old workflows. It also removes support for Python 3.7 and 3.8.

New Tools

• A new tool, pVACcompare allows users to visualize differences between output files from different pVACtools versions. This tool may be useful when investigating changes to predicted neoantigens between versions in controlled experiments where enumerating and explaining such differences may be crucial, e.g. in clinical trials. The tool can be run using the pvactools compare command. For more information please see the Comparison Tool documentation.
• A new standalone command pvacseq create_peptide_ordering_form generates peptide ordering files (FASTA, annotated ordering Excel spreadsheet, and review template Excel spreadsheet) to streamline preparation of peptides for synthesis and review. For more information please see the documentation

New Features

• pVACseq and pVACsplice now take into account the MANE Select and Canonical status of a transcript for filtering, prioritizing, and tiering a neoantigen candidate. MANE Select, Canonical, and TSL status is evaluated according to the new --transcript-prioritization-strategy parameter. This parameter allows users to list one or more criteria (mane_select, canonical, tsl) to take into consideration. As part of this update the "transcript support level filter" has been renamed to "transcript filter" including the standalone command which is now pvacseq|pvacsplice transcript_filter instead of pvacseq|pvacsplice transcript_support_level_filter.
• The aggregate report tiers have been updated to add four new tier:
  • PoorBinder: candidate fails the binding criteria but passes all other critieria.
  • RefMatch: candidate has a reference match but passes all other criteria.
  • ProbPos: candidate has a problematic amino acid but passes all other criteria.
  • PoorTranscript: a candidate's best transcript is neither MANE Select, Canonical, nor meets the TSL cutoff (depending on the specified --transcript-prioritization-strategy; only available in pVACseq and pVACsplice).
• By default, transcripts where the FLAGS VEP annotation is set will now be filtered out before processing by pVACseq and pVACsplice. This field identifies transcripts where the CDS 5' or 3' is incomplete. A new parameter --allow-incomplete-transcripts has been added which can be used to replicate the previous behavior where such transcripts were included.
• The pVACsplice logic for aggregating variants in the aggregate report creation has been updated to aggregate neoantigen candidates from the same Junction together instead of using the Index.
• Output file names of the reports have been updated to include MHC_I/MHC_II/Combined prefixes for easier identification of the type of output file.

Bugfixes

• This release fixes a bug with sorting of pVACfuse output files.

Full Changelog: https://github.com/griffithlab/pVACtools/compare/v5.5.4...v6.0.0