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 #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 #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):

• Fix a bug in the Mutation Position/Pos column where proximal variants and certain inframe indels might result in the incorrect position(s) being identified. As part of this bugfix, the meaning of these columns has been updated (see above). by @susannasiebert in #1206
• Fix pVACvector bug that would result in not all junctional epitopes getting tested on clipping. by @susannasiebert in #1200
• Fix a pVACvector bug that would result in an error if the -k flag was not set in a run. by @susannasiebert in #1186
• Fix warning related to new lines in the mouse anchor data files in pVACview. by @ldhtnp in #1184
• Fix the column tooltips in pVACview which were previously shifted by a couple of columns. by @ldhtnp in #1189
• Fix description of the ref_fasta positional parameter in pvacsplice. by @mhoang22 in #1201
• Fix description of pVACvector parameters. by @susannasiebert in #1208
• Fix an issue in pVACsplice which would throw an error with non-human transcripts. by @mhoang22 in #1198