5.0.1

What's Changed

• The --aggregate-inclusion-count-limit was not being passed along to the aggregate report module in the pVACsplice pipeline correctly. This release fixes that issue. by @susannasiebert in #1167

Full Changelog: v5.0.0...v5.0.1

5.0.0

This is a major version release. Please note that pVACtools 5.0 is not guaranteed to be backwards-compatible and certain changes could break old workflows.

New Tools

• This release adds a new tool, pVACsplice, for prediction neoantigens from splice sites. Please see the full tool documentation for more information. by @mrichters in #911

New Features

• This release refactors the pVACvector graph building algorithm in order to increase the probability for finding a solution and reduce the number of iterations needed before a solution is found. Please see the PR description for the full details. by @susannasiebert in #1163
• Add a new --aggregate-inclusion-count-limit parameter to set the maximum number of epitopes to include in the metrics.json detailed data for variants that have a large number of candidate neoantigens (e.g., frameshifts). by @susannasiebert in #1147
• Add a new --biotypes parameter which defines a list of transcript consequence biotypes that the predictions from pVACseq and pVACsplice should be limited to. by @mrichters in #911
• Add support for additional alleles that weren’t previously supported, includings ones for dog, mouse, and MHC class II. by @susannasiebert in #1148

Bugfixes

• This relase fixes a bug with the --agregate-inclusion-binding-threshold which would not be used if the --allele-specific-binding-thresholds flag was set. by @susannasiebert in #1147
• The pVACview percentile plots have been updated to include percentiles from elution and immunogenicity algorithms. by @susannasiebert in #1149
• This release fixes a bug where the incorrect neoantigen fasta entry may be used for the reference proteome search if there were multiple variants or alt alleles located at the same genomic position. by @susannasiebert in #1153
• Add additional trailing amino acids for frameshift insertions when creating fasta in order to capture a matched wildtype entry in large repetitive regions. by @susannasiebert in #1155

New Contributors

• @mrichters made their first contribution in #911

Full Changelog: v4.4.1...v5.0.0

4.4.1

What's Changed

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

• Previously, pVACview would add an additional header line to Excel spreadsheets when exporting a TSV. This has been fixed so that the first line in the spreadsheet is the actual header line. by @susannasiebert in #1143
• One of the pVACview figures used to describe various anchor scenarios has been updated so that the ordering of the scenarios is consistent with other figures and descriptions throughout. Screenshots and documentation has been updated appropriately. by @susannasiebert in #1144
• The class II pVACview demo data was out-of-date and not reflecting recent updates to the HLA alpha-beta chain handling. This file has now been updated. by @susannasiebert in #1145

Full Changelog: v4.4.0...v4.4.1

4.4.0

What's Changed

This is a minor feature release. It adds the following features:

• Various updates to the pVACview main interface:
  • Users can no select a row to investigate by clicking on the row
  • Users are now able to select an evaluation for a candidate by clicking on one of three buttons on the right of the candidate’s row.
• Various updates to the pVACview NeoFox interface:
  • By default, only a subset of NeoFox columns will be shown in order to reduce the width of the table. Additional columns can be enabled by selecting them in the “Column visibility” dropdown.
  • We have added heatmap cell backgrounds to IC50 binding affinity and rank columns.
  • We have added horizontal barplot background to VAF and expression columns.
  • Users are now able to select an evaluation for each candidate.
  • Users are now able to leave a comment on selected candidates.
  • The NeoFox table, including the selected evaluations and comments, can now be exported in TSV and excel format.

by @susannasiebert and @evelyn-schmidt in #1137

This release also fixes the following bug(s):

• A previous change would no longer allow standalone alpha/beta chain DP and DQ alleles. This change would filter out such alleles before trying to combine them into valid alpha-beta-chain pairs. This update once again enables automatic combination of DP and DQ alleles in to alpha and beta chain pairs. by @susannasiebert in #1139

Full Changelog: v4.3.0...v4.4.0

4.3.0

What's Changed

This is a minor feature release. It adds the following features:

• Add a new helper command pvacseq|pvacfuse|pvacbind|pvacvector valid_algorithms by @ldhtnp in #1108
• When running the pvacseq generate_protein_fasta command with the --phased-proximal-variants-vcf argument, output the intermediate proximal_variants.tsv file by @evelyn-schmidt in #1091
• In pVACview, clear the comment text input box after saving the comment by @ldhtnp in #1113
• Add support for mouse allele anchor positions by @ldhtnp in #1110
• Skip variants where VEP didn’t predict an amino acid change by @susannasiebert in #1121
• Update the ordering of the fasta file output of the pvacseq|pvacfuse generate_protein_fasta command when running with the --input-tsv argument so that the order of the fasta sequences is consistent with the order of the neoantigen candidates in the input TSV by @mhoang22 in #1002
• Update the pvacfuse generate_protein_fasta command to allow aggregated TSVs as an input TSV by @susannasiebert in #1134
• Update pVACview to display the anchor positions currently applied to the data by @susannasiebert in #1114

This release also fixes the following bug(s):

• Handle invalid pVACfuse characters by trimming the sequence instead of skipping it. The previous implementation would lead to missing sequences in certain downstream steps, resulting in errors. by @susannasiebert in #1130
• Add new pVACview R files to the list of files getting copied into the pVACseq output folder. These files were previsouly not copied in the the results folder, leading to error when running the pvacview run commands on a pVACseq output directory. by @susannasiebert in #1126
• Remove single DP and DQ alpha and beta chain alleles from the list of supported alleles in MHCnuggetsII. This is because those alleles need to be defined as a pair of alpha- and beta-chains in order to be meaningful. Also remove DRA alleles from the same list since the DR locus is defined only by the beta chain because functional variation in mature DRA gene products is absent. by @susannasiebert in #1133
• Fix errors in the rounding of the min and max values of the sliders in the custom pVACview module by @evelyn-schmidt in #1116
• Remove unused code in the Frameshift.pm VEP plugin that causes errors with certain types of variants by @susannasiebert in #1122

New Contributors

• @ldhtnp made their first contribution in #1108
• @mhoang22 made their first contribution in #1002

Full Changelog: v4.2.1...v4.3.0

4.2.1

What's Changed

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

• When running the reference protome similarity step with a reference protome peptide fasta file and a species other than human or mouse, the run would be aborted with an error that the refseq_protein_prot BLASTp database was incompatible with the species. This error should not be emitted in this circumstance since BLASTp is not run when using a reference proteome peptide fasta file. This release fixes this error and allows users to run the reference proteome similarity step on non-human and non-mouse data with a reference proteome peptide fasta. by @susannasiebert in #1115

Full Changelog: v4.2.0...v4.2.1

4.2.0

What's Changed

This is a minor feature release. It adds the following features:

• We added two new modules to pVACview: a Neofox Module to visualize NeoFox neoantigen annotations and a Custom Module to visualize neoantigen data in a TSV file, for example output files from VaxRank, NeoPredPipe, or antigen.garnish. by @evelyn-schmidt in #1062
• We added a vignette to our documentation to provide an extended tutorial on how evaluate neoantigen candidates using pVACview. by @mhoang22 in #1062

This release also fixes the following bug(s):

• When running pVACfuse with Arriba input data, the 3’ transcript was not being parsed correctly. This release fixes this issue.
  by @susannasiebert in #1094

Full Changelog: v4.1.1...v4.2.0

4.1.1

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

• The previous version updated how the all_epitopes.tsv file was parsed when creating the aggregated report and NA values are now parsed as native pandas nan. However, this update was not handled correctly for the Mutation Position column, leading to errors with NA values in that column. This release fixes this error. (#1079)
• The previous version would write the DeepImmuno output file in the same location for multiple prediction calls. This would lead to errors when running in multi-threaded mode. This releases updates the code to write DeepImmuno outputs to unique file locations. (#1078)
• This release updates how the list of combinatorial class II alleles is created in order to return it as a sorted list, creating a consistent order when writing the input.yml log file. (#1077)
• This release updates the GitHub commit for the pVACview demo data in order to pull the latest version of this data, including DeepImmuno and BigMHC prediction data. (#1073)
• This release fixes an issue where the pVACvector visualization images were saved in a low resolution format resulting in blurry images. (#1071)
• This release fixes an issue where the method to determine the matched wildtype result didn’t return where appropriate, causing the mutation position to not be set correctly. (#1082)
• This release fixes some typos. (#1072)

4.1.0

This is a minor feature release. It adds the following features:

• This release adds support for two new prediction algorithms: BigMHC and DeepImmuno (#1063). BigMHC includes predictions for elution (BigMHC_EL) and immunogenicity (BigMHC_IM). DeepImmuno is a prediction algorithms for immunogenicty.

• This release includes several updates to pVACview (#1012):

  • The tab containing the anchor heatmaps for each well-binding peptide of a variant has been moved to the “Transcript and Peptide Set Data” panel.
  • The anchor heatmap tab now also contains a table of all the per-length and per-allele anchor weights for each position in a peptide.
  • The pVACtools version is now displayed at the bottom of the sidebar.
  • A new panel has been added to show the tiering parameters currently applied.
  • Where there are multiple transcript sets for a variant, the one containing the best peptide is now selected by default.

• This release adds a new command pvactools download_wdls (#1055). This command can be used to download WDL workflow files for pVACseq and pVACfuse.

4.0.8

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

• pVACbind was not parsing the individual El prediction algorithm scores correctly resulting in them being missing from the all epitopes file.
• This release fixes some display issues in pVACview. It also implements a Docker file and bash script for deploying pVACview to GCP.