Version 1.4


This version adds the following features:

  • pVACvector now tests spacers iteratively. During the first iteration, the first spacer in the list of --spacers gets tested. In the next iteration, the next spacer in the list gets added to the pool of spacers to tests, and so on. If at any point a valid ordering is found, pVACvector will finish its run and output the result. This might result in a slightly less optimal (but still valid) ordering but improves runtime significantly.

  • If, after testing all spacers, no valid ordering if found, pVACvector will clip the beginning and/or ends of problematic peptides by one amino acid. The ordering finding process is then repeated on the updated list of peptides. This process may be repeated a number of times, depending on the value of the --max-clip-length parameter.

  • This version adds a standalone command to create the pVACvector visualizations that can be run by calling pvacvector visualize using a pVACvector result file as the input.

  • We removed the --aditional-input-file-list option to pVACseq. Readcount and expression information are now taken directly from the VCF annotations. Instructions on how to add these annotations to your input VCF can be found on the Input File Preparation page.

  • We added support for variants to pVACseq that are only annotated as protein_altering_variant without a more specific consequence of missense_variant, inframe_insertion, inframe_deletion, or frameshift_variant.

  • We resolved some syntax differences that prevented pVACtools from being run under python 3.6 or python 3.7. pVACtools should now be compatible with all python >= 3.5 versions.


This is a hotfix release. It fixes the following issues:

  • In version 1.4 we updated our usage of conda to use conda activate instead of source activate to make it compatible with newer conda versions. However, this was leading to errors due to the way that we were calling conda. This has been updated and should resolve these types of errors.


This is a hotfix release. It fixes the following issues:

  • This releases fixes a concurrency issue with pVACapi/pVACviz that would occurr when users would try to visualize multiple files at the same time.


This is a hotfix release. It fixes the following issues:

  • IEDB will output a warning if an epitope contains only amino acid symbols that could also be nucleotides. This would cause an error during parsing of the IEDB output files. This version updates the parser to ignore these warnings.

  • We added some improvements to pVACapi regarding database file read speeds and transaction handling.


This is a hotfix release. It fixes the following issues:

  • This version starts enforcing a file size limit (14MB) to be able to visualize a result file in pVACviz. Larger files will no longer be visualizable in pVACviz since they take too long to load.


This is a hotfix release. It fixes the following issues:

  • In a previous version we implemented a faster method for reading data from the database in pVACapi. However, this would fail if the postgres user is not a superuser. This version fixes this issue by using the previous database file read method in this situation.

  • This version marks certain columns of the output reports as not visualizable in pVACviz/pVACapi because they contain string content that cannot be plotted in a scatterplot.