Version 5.2

Version 5.2.0

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

  • Add a new parameter --percentile-threshold-strategy that controls filtering and tiering behavior when a percentile threshold is set. If this parameter is set to conservative a candidate has to pass both the binding affinity and percentile score thresholds. If it is set to exploratory it only has to pass either the binding affinity or the percentile score threshold. by @ldhtnp in https://github.com/griffithlab/pVACtools/pull/1185

  • Add a new parameter --netmhciipan-version that controls which version of NetMHCIIpan and NetMHCIIpanEL are being run. The default remains version 4.1. by @ldhtnp in https://github.com/griffithlab/pVACtools/pull/1181

  • The meaning of the Mutation Position column (in the all_epitopes.tsv and filtered.tsv pVACseq reports) and the Pos column (in the aggregated pVACseq report) has been updated to reflect the position(s) in the mutant epitope that are different from the matched wildtype epitope.

    • This is different from the previous behaviors, particular for indels, where previously this column was trying to reflect where the mutation occurred. However, this has proven difficult to programmatically determine correctly for cases with proximal variants, in repetitive regions, or where the mutant amino acid(s) are similar the wildtype amino acid(s).

    • For inframe indels, this change might now result in some positions getting marked as different from the matched wildtype amino acid even though they aren’t technically part of the variant because wildtype amino acids are shifted in relation to the mutant in this type of variants. These shifted amino acids, although not mutated, are now different between mutant and matched wildtype epitope and marked as such. We do believe that this is the better approach because it allows us to evaluate the absolute differences between the matched wildtype and mutant epitopes.

    • These columns are now always NA if the wildtype epitope is NA

    • For making the anchor position evaluation, epitopes with more than two Mutation Position/Pos entries are auto-passed.

It also fixes the following problem(s):