Update documentation

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
+<https://github.com/griffithlab/pVAC-Seq/issues/323>`_ 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
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