Version 5.4¶

Version 5.4.0¶

This is a minor feature release. It adds the following features:

Add functionality to add gene of interest identification. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1229

A new option --genes-of-interest-file has been added. This option allows users to specify a file path containing genes name that are of particular importance to their research. Neoantigens resulting from variants on one of these genes will be marked in the all_epitopes.tsv and filtered.tsv files in a new Gene of Interest column (True/False). If this option is not specified, a default list of common cancer genes is used.

This is a bugfix release. It fixes the following problem(s):

Ensure that the files in the supporting_files directory, including the default genes of interest list, are included in the distribution Otherwise the Mark Genes Of Interest step would fail with a file-not-found error.

This is a bugfix release. It fixes the following problem(s):

Handle cases where the peptide sequence for a variant is missing from the fasta during reference proteome similarity matching. Instead of throwing in error, skip such entries and mark Ref Prot column as “Not Run”. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1253
Write a log message for the above cases. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1259
Fix bug in processing inframe deletions during aggregation causing the variant type to not be set correctly. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1255
Respect --anchor-types parameter in pVACsplice. Previously, even when specifying this parameter it would be ignored and a hard-coded list of anchors would be used. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1258
Update description of the --starfusion-file parameter to reflect that it can be used with Arriba data. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1263

This is a bugfix release. It fixes the following problem(s):

Fixed IC50/%ile WT sorting to use numerical sorting instead of string sorting. by @ldhtnp in https://github.com/griffithlab/pVACtools/pull/1265
Bugfixes for the pvacsplice generate_protein_fasta command to handle sequences shorter than the flanking sequence length and sequences with unsupported amino acids. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1268