Version 5.0

Version 5.0.0

This version adds the following features, outlined below. 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 https://github.com/griffithlab/pVACtools/pull/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 describtion for the full details. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/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 https://github.com/griffithlab/pVACtools/pull/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 https://github.com/griffithlab/pVACtools/pull/911

• Add support for additional alleles that weren’t previously supported, includings ones for dog, mouse, and MHC class II. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/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 https://github.com/griffithlab/pVACtools/pull/1147

• The pVACview percentile plots have been updated to include percentiles from elution and immunogenicity algorithms. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/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 https://github.com/griffithlab/pVACtools/pull/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 https://github.com/griffithlab/pVACtools/pull/1155

Version 5.0.1

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

• 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 https://github.com/griffithlab/pVACtools/pull/1167