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.