Version 3.0

Version 3.0.0

This version adds the following features, outlined below. Please note that pVACtools 3.0 is not backwards-compatible and certain changes will break old workflows.

Breaking Changes

  • The pVACapi and pVACviz tools have been removed. They have been replaced by the pVACview tool.

  • The package namespace has been updated. The files will now be installed underneath a pvactools directory in your python package installation path.

  • The aggregated report format has been updated. The headers have been updated for clarity. An additional column Allele Expr has been added, representing RNA expression * RNA VAF. For more information see all_epitopes.aggregated.tsv Report Columns.

  • pVACfuse no longer supports inputs from Integrate NEO. Only AGFusion inputs will be supported going forward.

  • The format of the pVACfuse all_epitopes and filtered reports has been updated to remove columns that aren’t applicable for the tool. Please see the documentation for the pVACfuse Prediction Algorithms Supporting Percentile Information for more information.

New Features

  • This release adds a new tool, pVACview. pVACview is an R Shiny application that allows for that visualization of the pVACseq aggregated report file to review, explore, and prioritize the different neoantigen candidates predicted by pVACseq.

  • The 3.0 release adds several improvements to the reference proteome similarity step:

    • Users can now run the reference proteome similarity step with a standalone Protein BLAST installation. To use a standalone BLASTp installation, provide the installation path using the --blastp-path parameter. The supported Protein BLAST databases are refseq_select_prot and refseq_protein. Please reference the Installing BLAST documentation for further instructions.

    • When running the reference proteome similarity step using the NCBI Protein BLAST API, users can now pick between the refseq_select_prot and refseq_protein databases.

    • Parallelization has been added to the reference proteome similarity step. When running this step as part of the pVACseq, pVACfuse, or pVACbind pipelines, the existing --t parameter will also be used to set the number of parallel threads in this step.

  • This release adds standalone commands to run stability predictions, cleavage site predictions, and the reference proteome similarity step on the output of the pVACseq, pVACfuse, and pVACbind pipelines.

Minor Updates

  • Previously, when running NetChop for cleavage site predictions, predictions were made for each epitope individually. However, these predictions will differ if additional flanking amino acids are provided and will be stable with 9 or more flanking amino acids. We updated this step to make predictions with 9 flanking amino acids around each epitope to generate stable predictions.

  • This release adds a --species option to the valid_alleles commands to filter alleles on a species of interest.

  • This release adds a --pass-only flag to the pvacseq generate_protein_fasta commands to only process VCF entries that do not have a FILTER set.

  • This release adds a new parameter --tumor-purity. This parameter indicates the fraction of tumor cells in the tumor sample and is used during aggregate report creation for a simple estimation whether variants are subclonal or clonal based on VAF.

Version 3.0.1

This is a bugfix release. It fixes the following problem(s):

  • There was small issue in pVACview where picking a different number of variants in the main table would cause changes to variant evaluations to not be recorded correctly.

  • This release also fixes a problem where loading a new set of files into pVACview would not reset previous evaluation summary counts.

  • This release fixes an error in pVACtools that would occur when a chromosomal region in the somatic VCF is not present in the proximal VCF.

  • This release adds further error checking for malformed CSQ header descriptions.

  • This release updates various code portions to remove deprecation warnings and add support for newer versions of certain dependencies (e.g. pandas).

  • This release fixes an bug with the standalone pvacseq calculate_reference_proteome_similarity command where picking a custom --match-length would throw an error.

  • Some users were reporting errors during the tmp file cleanup stages of running the various pipelines. This releases fixes that issue.

Version 3.0.2

This is a bugfix release. It fixes the following problem(s):

  • Newer versions of Ensembl annotations added genes without a HUGO gene name. Variants on those genes cause downstream errors in the aggregate report creation when running the pVACseq pipeline. This release fixes this error.

Version 3.0.3

This is a bugfix release. It fixes the following problem(s):

  • When using the --additional-report-columns parameter in pVACview/pVACfuse, no contents were previously written to the additional columns.

  • MHCflurry may return no value for the percentile binding score. This would previously result in an error which has been fixed in this release.

  • Variants in a VCF may contain an empty AF field, which was previsouly not being handled correctly in all cases, resulting in an error.

This release also includes some minor improvements:

  • When running the pVACseq pipeline there would be a lot of warning messages about missing position column parameters. These would mostly be noise because the underlying consequence type wasn’t supported by pVACseq to begin with. This release removes these warning messages for mutations with consequences that are not supported by pVACseq.

Version 3.0.4

This is a bugfix release. It fixes the following problem(s):

  • This fixes an issue introduced in the previous release where VCF entries with no VAF value would result in an error.

  • This release adds a new constraint to the vaf cutoff command line arguments to ensure that they are a fraction between 0 and 1.

  • This release also fixes an issue where the wrong binding filter class was being used when running pVACfuse with allele-specific binding cutoffs.