From 8dde1e8d76ebfdd8f2ab0cf1dcf80cb792729cee Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Tue, 5 Sep 2017 08:55:38 -0500 Subject: [PATCH] Update documentation --- docs/index.rst | 32 ++++++++++---------------------- 1 file changed, 10 insertions(+), 22 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index 13ab162..fb3dbac 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -24,28 +24,16 @@ pVAC-Seq is a cancer immunotherapy pipeline for the identification of **p**\ ers New in version |version| ------------------------ -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. +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. Citation --------