pVAC-Seq v4.0.0

• Support for MHC Class II predictions
• Integration of NetChop cleavage site predictions and NetMHCstab stability predictions
• Support for bam-readcount and Cufflinks input files to provide coverage data

pVAC-Seq v3.0.5

• Bugfix: The generation of the fasta file would fail for some insertions with a range position. This is now fixed.
• Bugfix: The generation of the fasta file would fail if the wildtype or downstream sequences were too long. The size limit for these fields has been increased to the user system's maximum supported size. This error might still occur if the sequences are longer than that.
• Bugfix: When rerunning a command an error would occur if the tmp subdirectory already exists in the output directory. This has now been fixed.

pVAC-Seq v3.0.4

• Certain intermediate files are now written into a tmp directory underneath the main output directory. This tmp directory will be deleted at the end of a successful run unless the --keep-tmp-files flag is set.
  Intermediate files will now not be reprocessed if they already exist in the output directory. This can be helpful if a run exits early, for example, when a 500 Error was returned by IEDB. In this case the user can now simply run the same pvacseq run command again and the run will pick up where it failed previously.
• We added a new option --fasta-size that the user can set to specify how many FASTA entries at a time will be included in a request to the IEDB RESTful API. The default is 200 but certain variants or prediction algorithms might warrant a smaller number of FASTA entries in order to avoid timeouts from IEDB.
• Bugfix: The parsing step would fail for frameshift mutations with a range position. This is now fixed.
• Bugfix: Previously a run might fail if certain intermediate files weren't created.
• Bugfix: Using . in the output directory name and the sample name would previously result in errors. This has now been fixed.
• Bugfix: Using a relative directory path for the output directory would previsouly result in an error. This is now fixed.

pVAC-Seq v3.0.3

• Bugfix: The binding filter used to filter out all but the top peptide candidate for a variant even if the --top-result-per-mutation flag wasn't set. This is now fixed and the top-result-per-mutation filtering only happens when the flag is set.
• Bugfix: For large input files the mutant protein sequence wasn't being correctly matched to a wildtype protein sequence. This issue has been corrected.

pVAC-Seq v3.0.2

• Bugfix: Some allele names in the list of valid alleles were incorrect. The list has been updated.
• If the generate_fasta step creates an empty file during the execution of a run the run will terminate early.

pVAC-Seq v3.0.0

• pVAC-Seq now uses the IEDB RESTful interface for making epitope binding predictions. A local install of NetMHC3.4 is no longer required. By using IEDB the user now has a choice between several prediction algorithms, including NetMHC (3.4), NetMHCcons (1.1), NetMHCpan (2.8), PickPocket (1.1), SMM, and SMMPMBEC.
• The user can now set the --top-result-per-mutation flag in order to only output the top scoring candidate per allele-length per mutation.
• Since it is now possible to run multiple epitope prediction algorithms at the same time, the scores for each candidate epitope are aggregated as Median MT score All Methods, which is the median mutant ic50 binding score of all chosen prediction methods, and the Best MT score, which is the lowest mutant ic50 binding score of all chosen prediction methods. For the Best MT score we also output the Corresponding WT score and the Best MT Score Method. Individual ic50 binding score for each prediction method are also outputted. The user can specify which metric to use for filtering by setting the --top-score-metric argument to either lowest or median.

pVAC-Seq v2.0.2

*Bugfix: There was a problem in version 2.0.1 where pVAC-Seq would hang while calling NetMHC under certain cirumstances. This is now fixed.
*Bugfix: When using multiple alleles or epitope lengths, pVAC-Seq would not output all candidate epitopes after running the binding filter. This has now been fixed.

pVAC-Seq v2.0.0

*Supports inframe indels and frameshifts
*Supports VCF as the input file format

Convert scripts to Python 3

Merge pull request #46 from griffithlab/python

Python

First stable release in Perl

v1.0.0

First stable version in Perl.