griffithlab/pVACtools: 3.0.0

This version adds the following features, outlined below. Please note that pVACtools 3.0 is not backwards-compatible and certain changes will break old workflows. Breaking Changes The pVACapi and pVACviz tools have been removed. They have been replaced by the pVACview tool. The package namespace has been updated. The files will now be installed underneath a pvactools directory in your python package installation path. The aggregated report format has been updated. The headers have been updated for clarity. An additional column Allele Expr has been added, representing RNA expression * RNA VAF. For more information see all_epitopes.aggregated.tsv Report Columns pVACfuse no longer supports inputs from Integrate NEO. Only AGFusion inputs will be supported going forward. The format of the pVACfuse all_epitopes and filtered reports has been updated to remove columns that aren't applicable for the tool. Please see the pVACfuse output file documentation for more information. New Features This release adds a new tool, pVACview. pVACview is an R Shiny application that allows for that visualization of the pVACseq aggregated report file to review, explore, and prioritize the different neoantigen candidates predicted by pVACseq. The 3.0 release adds several improvements to the reference proteome similarity step: Users can now run the reference proteome similarity step with a standalone Protein BLAST installation. To use a standalone BLASTp installation, provide the installation path using the --blastp-path parameter. The supported Protein BLAST databases are refseq_select_prot and refseq_protein. Installation instructions for BLAST can be found here. When running the reference proteome similarity step using the NCBI Protein BLAST API, users can now pick between the refseq_select_prot and refseq_protein databases. Parallelization has been added to the reference proteome similarity step. When running this step as part of the pVACseq, pVACfuse, or pVACbind pipelines, the existing --t parameter will also be used to set the number of parallel threads in this step. This release adds standalone commands to run stability predictions, cleavage site predictions, and the reference proteome similarity step on the output of the pVACseq, pVACfuse, and pVACbind pipelines. Minor Updates Previously, when running NetChop for cleavage site predictions, predictions were made for each epitope individually. However, these predictions will differ if additional flanking amino acids are provided and will be stable with 9 or more flanking amino acids. We updated this step to make predictions with 9 flanking amino acids around each epitope to generate stable predictions. This release adds a --species option to the valid_alleles commands to filter alleles on a species of interest. This release adds a --pass-only flag to the pvacseq generate_protein_fasta [command] (https://pvactools.readthedocs.io/en/latest/pvacseq/additional_commands.html#list-valid-alleles) to only process VCF entries that do not have a FILTER set. This release adds a new parameter --tumor-purity. This parameter indicates the fraction of tumor cells in the tumor sample and is used during aggregate report creation for a simple estimation whether variants are subclonal or clonal based on VAF