pVAC-Seq v4.0.10

This is a hotfix release to fix a bug with how certain types of frameshift mutations were handled. Previously, we were not creating the correct mutant peptide sequence for these variants. See this GitHub issue for more information.

This version also includes a sanity check to error out if the wildtype amino acid in the wildtype protein sequence differs from the expected wildtype amino acid as listed in the protein change. This situation might occur if the VCF was annotated with a different reference build than the one used for alignment and variant calling.

pVAC-Seq v4.0.9

This release adds handling for DNPs and MNPs missense mutations.

This version adds a new option --additonal-report-columns to the pvacseq run command which can be use to append additional columns of data to the report. Right now the only value supported for this option is sample_name which appends a column with the sample name to the final report.

We updated the logic that determines whether or not a corresponding wildtype epitope for a mutant epitope is included in the report. Previously, we would only include the corresponding wildtype epitope if the number of consecutive matching amino acids between mutant and wildtype epitope was larger then half of the total number of amino acids in the epitope. We now use the total number of matching amino acids between the mutant epitope and the corespondig wildtype epitope across the whole length of the epitope to make that determination. The total number of matching amino acids needs to be larger than half of the length of the epitope. Otherwise the corresponding wildtype epitope is reported as “NA”.

With this release any execution of pvacseq run will create a log file of the inputs used. This log file is then used when executing another run with the same output directory. This ensures that you can only write to the same output directory if identical parameters are used.

pVAC-Seq v4.0.8

This is a hotfix release. It fixes an error introduced in a previous version that would occur when using a local installation of the IEDB tools and is related to some filtering we do on the output from the IEDB tools. More information can be found on GitHub issue #278.

pVAC-Seq v4.0.7

This version improves the sorting of the final report file. The file will now be sorted by “Gene Name” and “Mutation” and within these categories by the MT score - either “Median MT Score” or “Best MT score” depending on the top-score-metric used.

This release implements a 60 second wait between each request to the IEDB RESTful API in order to decrease the load on their servers. We recommend the usage of the standalone IEDB tools for long-running processes with many variants, prediction algorithm, epitope lengths, or alleles.

There also have been various bugfixes in this release.

pVAC-Seq v4.0.6

This version updates the IEDB RESTful API URL to the new target announced in IEDB Analysis Resource v2.15.1.

This release introduces a change in how invalid alleles are handeled. Previously, the pipeline would throw a fatal error. The pipeline will now proceed but invalid alleles will be skipped.

This version also has improved error handling around calling standalone IEDB installations.

pVAC-Seq v4.0.5

This release fixes a couple of bugs related to the processing of frameshift variants.

pVAC-Seq v4.0.4

This release fixes a couple of minor bugs. Firstly, the pipeline will now skip variants that result in the loss of a start codon. Secondly, this release fixes a bug that would result in an error when the input VCF doesn’t contain any sample genotype information. VCFs with no samples will now be fully processed through the pipeline.

pVAC-Seq v4.0.3

We added an optional downstream analysis tool to generate an annotated fasta file from a VCF with protein sequences of mutations and matching wildtypes. This tool can be run with the pvacseq generate_protein_fasta command.

This release fixes a couple of errors that were introduced in the previous version which would occur during the processing of certain inframe indels.

This version also fixes an error that would occur if the number of variants to process was a multiple of the chosen --fasta-size.

pVAC-Seq v4.0.2

pVAC-Seq now supports local installs of IEDB MHC class I (http://tools.iedb.org/mhci/download/) and class II (http://tools.iedb.org/mhcii/download/) binding prediction tools. This feature can be used by passing the directory that contains the local installations to the --iedb-install-directory parameter.

This version adds a new column Mutation Position to the report output. This column denotes the 1-based start position of the mutation in the MT Epitope Seq. If the value is 0 the mutation start position is before the first position in the epitope.

pVAC-Seq now allows the user to specify the number of retries after a request to the IEDB RESTful interface fails. The number of retries can be set by using the --iedb-retries parameter. Previously this number was hard-coded to 3. More retries might be necessary in order to get a successful response for complex queries (e.g., large number of variants, long frameshift downstream sequences, choice of compute-intensive prediction algorithms). This parameter should be used in conjunction with --fasta-size and --downstream-sequence-length for the highest likelihood of success of finishing a pVAC-Seq run.

This release fixes an error that was introduced in the previous version which would occur when the user would try to rerun a process in the same output directory.

This version also fixes a bug with how to handle variants that are no-call or homozygous-reference. These variants will now be skipped.

pVAC-Seq v4.0.1

This version fixes compatibility issues with the new IEDB Analysis Resource v2.15 that was released on October 3rd 2016. Since pVAC-Seq uses the IEDB RESTful web interface, the new IEDB Analysis Resource version is being used natively. As a result, pVAC-Seq output for the NetMHC prediction algorithm is now NetMHC version 4.0. Some other changes in the output format from IEDB led to compatibility issues that are fixed in this new pVAC-Seq release.

This release also fixes an error with bam-readcount input files that occurs when a variant does not have a bam readcount entry.