This version adds the following features, outlined below. Please note that pVACtools 2.0 is not backwards-compatible and certain changes will break old workflows.
Breaking changes
- pVACtools now supports variable epitope lengths for class II prediction algorithms. The previous option `--epitope-length` (`-e`) no longer exists. It has been replaced with `--class-i-epitope-length` (`-e1`) and `--class-ii-epitope-length` (`-e2`) for class I and class II epitope lengths, respectively. The defaults are `[8, 9, 10, 11]` and `[12, 13, 14, 15, 16, 17, 18]`, respectively.
- The `--peptide-sequence-length` option has been removed. The peptide sequence length is now determined by the epitope length(s) to determine the flanking sequence length before and after the mutation.
- pVACtools no longer depends on conda. pVACtools remains compatible with Python 3.5 and above but users may chose any environment manager to set up an appropriate Python environment.
- When using standalone IEDB, pVACtools is now only compatible with IEDB 3.1 and above. Please see [Installation](https://pvactools.readthedocs.io/en/latest/install.html#install) for instructions on installing the latest IEDB version.
- pVACseq is no longer dependent on annotations with the VEP Downstream plugin. This dependency has been replaced with the VEP Frameshift plugin. This requires changes to your existing VEP installation in order to install the Frameshift plugin. Existing VCFs that were previously annotated to work with pVACtools 1.5 and below will no longer work with version 2.0 and above and will need to be reannotated. Please see our documentation on [Annotating your VCF with VEP](https://pvactools.readthedocs.io/en/latest/pvacseq/input_file_prep/vep.html#vep) for more information.
- The `filtered.condensed.tsv` report has been removed and replaced with the `all_epitopes.aggregated.tsv` report. We believe that this new report will provide a more useful summary of your results. Please see the Output Files sections of each tool for more information on this new report.
New features
- pVACtools now provides binding affinity percentile rank information, in addition to the raw ic50 binding affinity values. Users may filter on the percentile rank by using the new `--percentile-threshold` argument.
- Users now have the option of calculating the reference proteome similarity of their filtered epitopes. For this, the peptide sequence for the remaining variants is mapped to the reference proteome using BLAST. Variants where this yields a hit to a reference proteome are marked accordingly and a .reference_matches file provides more information about the matches. This option can be enabled using the `--run-reference-proteome-similarity` option.
- Users may now use the options `all`, `all_class_i`, or `all_class_ii` instead of specific prediction algorithms in order to run all prediction algorithms, all class I prediction algorithms, or all class II prediction algorithms, respectively.
- For successful pVACvector runs, we now output a `_results.dna.fa` file with the most likely nucleic acid sequence for the predicted vector.
Minor Updates
- When running pVACseq with a proximal variants VCF we would previously assume that your ran VEP with the `--pick` option and only process the first transcript annotation for a variant. With this update we will now associate the correct transcript for a proximal variant with the matching transcript of the main somatic variant of interest.
- The `pvacseq generate_protein_fasta` command now allows users to provide a proximal variants VCF using the `--phased-proximal-variants-vcf` option.
- The `pvacseq generate_protein_fasta` command now supports multi-sample VCFs. Users may use the `--sample-name` to provide the sample name of the sample they wish to process.
- pVACseq and pVACfuse would previously error out if the intermediate TSV parsed from the input was empty. In 2.0 the tool will no longer error out but exit with an appropriate message.
- pVACvector would previously error out when no valid path was found. In 2.0 pVACvector will not longer error out but exit with an appropriate message.
- We now set consistent file permissions on all output files.
- We’ve updated our license to BSD 3-Cause Clear. Please note that the individual licenses of our dependent tools remain in place. These can be viewed by on the [Tools Used By pVACtools](https://pvactools.readthedocs.io/en/latest/tools.html#tools) page.