# pVACtools¶

pVACtools is a cancer immunotherapy tools suite consisting of the following tools:

pVACseq
A cancer immunotherapy pipeline for identifying and prioritizing neoantigens from a list of tumor mutations.
pVACfuse
A tool for detecting neoantigens resulting from gene fusions.
pVACvector
A tool designed to aid specifically in the construction of DNA-based cancer vaccines.
pVACviz
A browser-based user interface that assists users in launching, managing, reviewing, and visualizing the results of pVACtools processes.

## New in version 1.1.1¶

This is a hotfix release. It fixes the following issue(s):

• In version 1.1 we updated VAFs to be fractions, rather than percentages. A bug in this code change resulted in an error when using custom VAF cutoff values instead of the default. This has now been fixed.

## New in version 1.1¶

This version adds a host of new features to pVACtools:

• pVACseq is now able to parse VAF, depth, and expression information directly from the VCF. This makes the --additional-input-file-list option obsolete. The --additional-input-file-list option is now deprecated and will be removed in an upcoming release. For more information on how to annotate your VCF with readcount and expression information, see the Input File Preparation page.
• pVACseq is now able to handle proximal germline and somatic variants. In order to incorporate those into the epitope predictions, you will need to provide a phased variants VCF to your pVACseq run using the --phased-proximal-variants-vcf option. For more information on how to create this file, see the Input File Preparation page.
• We added support to pVACseq for filtering on transcript support levels. This requires the input VCF to be annotated with the TSL field by VEP. Be default, any transcripts with a TSL above 1 will be filtered out.
• The binding filter of pVACseq and pVACfuse can now be run with flexible, allele-specific binding-thresholds. This feature can be enabled using the --allele-specific-binding-thresholds flag. The thresholds used are taken from the IEDB recommendations.
• pVACseq now supports a --pass-only flag that will result in any VCF entries with a FILTER to be skipped. Using this flag, only VCF entries with a FILTER of PASS or . will be processed.
• We added support for the MHCflurry and MHCnuggets prediction algorithms. These can be used by listing MHCflurry, MHCnuggetsI (for MHC Class I alleles), and/or MHCnuggetsII (for MHC Class II alleles) as the prediction algorithms in your run commands.
• The default --tdna-vaf and --trna-vaf cutoff values have been updated from 0.4 to 0.25. This is the minimum VAF threshold that an epitope candidate must meet in order to pass the coverage filter.
• We now offer a graphical user interface, pVACviz, to run pVACseq as an alernative to using the command line. pVACviz, can also be used to plot and filter your pVACseq results.