4.0.5

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

• In recent releases, users have noticed that at some point during pipeline runs, predictions to MHCflurry would hang or get killed. We were able to determine that the cause was related to PR 988. This PR originally updated calls to MHCflurry to happen by instantiating their predictor within Python instead of calling it on the command line. However, we suspect that this causes a substantial increase in memory usage resulting in the observed behavior. This release reverts the change from PR 988.

4.0.4

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

• This release makes various fixes to allow pVACtools to run with non-human data.

4.0.3

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

• The fixes in issue in the reference proteome similarity step in pVACseq where running with non-human data would cause an error.

4.0.2

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

• Arriba annotated fusion sequences may contain characters that aren’t supported. This update skips such sequences.
• The --aggregate-report-evaluation parameter in the standalone pvacseq generate_protein_fasta command was previously set up with nargs in order to allow specifying multiple values. However, this conflicts with required positional parameters. The parameter definiton was updated so that multiple values are now specified as a comma-separated list.
• pVACfuse would previously fail in an odd way when none of the fusions in the input were processable. This update now exits pVACfuse more gracefully in this case.
• The reference proteome similarity step would previously fail when an epitope’s full peptide sequence wasn’t found in the input fasta. It now skips such epitopes and marks the Reference Match column as Not Run.
• There was a mismatch in how proximal variants were incorporated into the n-mer fasta files vs the “master” fasta file which had the potential of epitopes not being present in the “master” fasta file. This update brings both file creation steps in sync.

4.0.1

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

• It fixes errors for a few edge cases when determining the mutation position(s).
• Update the HCC1395 demo date for pVACview to include elution data.
• Correctly set NA columns in pVACview export dataframe.
• Handle Arriba files with empty peptide_sequence fields.

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.

3.1.3

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

• It fixes an issue with the reference proteome match step where stop lost mutations would throw a fatal error.

3.1.2

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

• It fixes an issue with parsing class II IEDB output files when running pVACfuse or pVACbind, which resulted in the wrong binding prediction scores being associated with certain epitopes.
• It adds missing import statements to pVACvector.

3.1.1

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

• The --exclude-NAs flag was not being passed along correctly to the main pipeline and didn’t have any effect on downstream filtering.
• The aggregate report creation step had some inefficiencies which caused its runtime to be much longer than necessary.
• An unneeded import statement for the PyVCF package had the potential to cause errors while running the pVACseq pipeline.

3.1.0

This release adds the following new features:

• When running the pipelines with the --netmhc-stab flag enabled, the NetMHCstab allele column now also reports the distance of the NetMHCstabpan allele when that allele is not identical to the HLA Allele of the original result.
• When running the pipelines with a set of individual class II alleles, the pipeline now also auto-generates valid combinations of these alleles so that users no longer need to explicitly provide these combinations.

This release also fixes the following problem(s):

• Some class I alleles are not supported by NetMHCstabpan and will lead to an error when attempt to make predictions with them. This release will skip such alleles for the stability prediction step.
• For very large result sets the filtering steps would stall or be killed because the steps would run out of memory. This release fixes this issue.
• This release adds better handling of timeout errors while running NetMHCstabpan and/or NetChop.