1.5.2

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

• AGFusion exon files may be comma-delimited. Previously, the file parser assumed the files were tab-delimited. This release now allows AGFusion inputs that are comma- or tab-delimited

1.5.1

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

• There was a syntax error in tools/pvacseq/generate_condensed_ranked_report.py that would result in an error when running the pvacseq generate-condensed-ranked-report commands.
• We were previously not correctly catching cases where the intermediate fasta for making binding prediction was empty. This would result in errors downstream.

1.5.0

This version adds the following features:

• This version introduces a new tool, pVACbind, which can be used to run our immunotherapy pipeline with a peptides FASTA file as input. This new tool is similar to pVACseq but certain options and filters are removed:
  • All input sequences are interpreted in isolation so corresponding wildtype sequence and score information are not assigned. As a consequence, the filter threshold option on fold change is removed.
  • Because the input format doesn’t allow for association of readcount, expression or transcript support level data, pVACbind doesn’t run the coverage filter or transcript support level filter.
  • No condensed report is generated.
  • Please see the pVACbind documentation for more information.
• pVACfuse now support annotated fusion files from AGFusion as input. The pVACfuse documentation has been updated with instructions on how to run AGFusion in the Prerequisites section.
• The top score filter has been updated to take into account alternative known transcripts that might result in non-indentical peptide sequences/epitopes. The top score filter now picks the best epitope for every available transcript of a variant. If the resulting list of epitopes for one variant is not identical, the filter will output all eptiopes. If the resulting list of epitopes for one variant are identical, the filter only outputs the epitope for the transcript with the highest transcript expression value. If no expression data is available, or if multiple transcripts remain, the filter outputs the epitope for the transcripts with the lowest transcript Ensembl ID.
• This version adds a few new options to the pvacseq generate_protein_fasta command:
  • The --mutant-only option can be used to only output mutant peptide sequences instead of mutant and wildtype sequences.
  • This command now has an option to provide a pVACseq all_eptiopes or filtered TSV file as an input (--input-tsv). This will limit the output fasta to only sequences that originated from the variants in that file.
• This release adds a pvacfuse generate_protein_fasta command that works similarly to the pvacseq generate_protein_fasta command but works with Integrate-NEO or AGFusion input files.
• We removed the sorting of the all_epitopes result file in order to reduce memory usage. Only the filtered files will be sorted. This version also updates the sorting algorithm of the filtered files as follows:
  • If the --top-score-metric is set to median the results are first sorted by the Median MT Score. If multiple epitopes have the same Median MT Score they are then sorted by the Corresponding Fold Change. The last sorting criteria is the Best MT Score.
  • If the --top-score-metric is set to lowest the results are first sorted by the Best MT Score. If multiple epitopes have the same Best MT Score they are then sorted by the Corresponding Fold Change. The last sorting criteria is the Median MT Score.
• pVACseq, pVACfuse, and pVACbind now calculate manufacturability metrics for the predicted epitopes. Manufacturability metrics are also calculated for all protein sequences when running the pvacseq generate_protein_fasta and pvacfuse generate_protein_fasta commands. They are saved in the .manufacturability.tsv along to the result fasta.
• The pVACseq score that gets calculated for epitopes in the condensed report is now converted into a rank. This will hopefully remove any confusion about whether the previous score could be treated as an absolute measure of immunogencity, which it was not intended for. Converting this score to a rank ensures that it gets treated in isolation for only the epitopes in the condensed file.
• The condensed report now also outputs the mutation position as well as the full set of lowest and median wildtype and mutant scores.
• This version adds a clear cache function to pVACapi that can be called by running pvacapi clear_cache. Sometimes pVACapi can get into a state where the cache file contains conflicting data compared to the actual process outputs which results in errors. Clearing the cache using the pvacapi clear_cache function can be used in that situation to resolve these errors.

1.4.5

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.

1.4.4

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.

1.4.3

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.

1.4.2

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

1.4.1

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.

1.4.0

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 order 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.

1.3.7

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

• The previous version accidentally removed the --additional-input-file-list option. It has been restored in this version. Please note that it is slated for permanent removal in the next feature release (1.4.0).