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@susannasiebert susannasiebert released this 18 Dec 20:18
· 41 commits to master since this release
v5.0.0
0e48fc7

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

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

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

Contributors

susannasiebert and mrichters
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