- pVAC-Seq now uses the IEDB RESTful interface for making epitope binding predictions. A local install of NetMHC3.4 is no longer required. By using IEDB the user now has a choice between several prediction algorithms, including NetMHC (3.4), NetMHCcons (1.1), NetMHCpan (2.8), PickPocket (1.1), SMM, and SMMPMBEC.
- The user can now set the `--top-result-per-mutation flag` in order to only output the top scoring candidate per allele-length per mutation.
- Since it is now possible to run multiple epitope prediction algorithms at the same time, the scores for each candidate epitope are aggregated as `Median MT score All Methods`, which is the median mutant ic50 binding score of all chosen prediction methods, and the `Best MT score`, which is the lowest mutant ic50 binding score of all chosen prediction methods. For the `Best MT score` we also output the Corresponding WT score and the `Best MT Score Method`. Individual ic50 binding score for each prediction method are also outputted. The user can specify which metric to use for filtering by setting the `--top-score-metric` argument to either `lowest` or `median`.