1.3.1

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

• Some prediction algorithms might predict a binding affinity of 0 which could lead to division by 0 errors when calculating the fold change. In this situation we now set the fold change to inf (infinity).
• Previously the --maximum-transcript-support-level threshold was not getting propagated to the main pipeline step correctly, resulting in errors in the transcript support level filter.
• There was a bug in the multiprocessing logic that would result in certain steps getting executed more than once, which in turn would lead to FileNotFound errors when these duplicate executions were happening at the same time.

1.3.0

This version adds a few features and updates:

• pVACvector now accepts a list of spacers to use when testing junction epitopes. These can be specified using the --spacers parameter with a comma-separated list of spacer peptides. Including the string None will also test each junction without spacers. The default is None,HH,HHC,HHH,HHHD,HHHC,AAY,HHHH,HHAA,HHL,AAL
• The --expn-val cutoff parameter has been updated to be a float instead of an integer. This allows the user to provide a decimal cutoff for the filtering on gene and transcript expression values. Previously, only whole numbers were accepted.
• Decimal numbers in the pVACseq reports are now rounded to three decimal places. Previously, they were not rounded.

In addition, this version also fixes a few bugs:

• The --normal-vaf cutoff value was incorrectly defaulting to 0.2 instead of 0.02. This resulted in the coverage filter not being as stringent as it should’ve been.
• There were a number of bugs in pVACapi and pVACviz that would prevent a user from submitting jobs using the interface in certain conditions. These have been resolved.
• pVACseq would previously not support SVs in the input VCF where the alt had a value of <DEL>. These kinds of variants are now supported.

1.2.0

This version introduces multiprocessing to pVACtools. This significantly speeds up the execution of pVACseq, pVACfuse, and pVACvector. To turn on multiprocessing simply set the --n-threads parameter to the desired number of parallel processes. When running the tools using the IEDB RESTful API, we recommend to keep this number small (<5) as too many parallel calls to their API might lead to IEDB blocking jobs submitted from your IP address. It is recommended to use a standalone IEDB installation when running in multiprocessing mode. By default, multiprocessing is turned off.

This version also fixes a few bugs:

• In certain cases pVACvector was not calculating the junction scores correctly, leading to potentially finding a peptide order that would include high-binding junction epitopes or peptide orders that were not optimal. This issue has now been fixed.
• Due to a bug in our packaging code, the 1.1.x versions of pVACtools did not include the latest version of the pVACviz code. This version now includes the most up-to-date version of the graphical user interface.

1.1.5

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

• When running pVACseq with a phased input VCF the mutation position offset of a frameshift somatic variant to their proximal variants was not getting calculated correctly, leading to errors.
• For running pVACvector we removed a dependency on a commandline tool by using a python library instead. This allowed us to remove a system call to a tool that required standalone installation by the user.

1.1.4

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

• When running pVACvector with a with a pVACseq input file and the corresponding VCF, the sample name wasn’t being passed along correctly which would cause an error if the input VCF was a multi-sample VCF.
• pVACseq would throw an error if the value of a gene or transcript expression field was empty.

1.1.3

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

• When using the MHCnuggets prediction algorithm for MHC class II alleles (MHCnuggetsII) not all epitope sequences were predicted for inframe insertions. This issues has now been fixed.
• For MHCflurry, cases with peptide sequences that were shorter than the desired epitope length were not handled correctly which resulted in an error. This issue has been resolved in this release.

1.1.2

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

• In version 1.1.0 we added a --pass-only flag to pVACseq that would result in only variants with FILTER of PASS or . getting processed. However, this option was not getting passed along to the pVACseq process correctly, resulting in this option not taking effect. This hotfix release fixes this issue and the --pass-only flag should now work as expected.

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.

1.1.0

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.

1.0.8

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

• The log directories were accidentially included with the pVACseq example data. They are now removed.
• Some users were reporting mixed type warnings for pandas when running pVACseq. We added some options to avoid this warning.