This version adds a few features and updates:
- pVACvector now accepts a list of spacers to use when testing junction
epitopes. These can be specified using the
--spacersparameter with a comma-separated list of spacer peptides. Including the string
Nonewill also test each junction without spacers. The default is
--expn-valcutoff parameter has been updated to be a float instead of an integer. This allows the user to provide a decimal cuttoff for the filtering on gene and transcript expression values. Previously, only whole numbers were accepted.
- Decimal numbers in the pVACseq reports are now rounded to three decimal places. Previously, they were not rounded.
In addition, this version also fixes a few bugs:
--normal-vafcutoff value was incorrectly defaulting to 0.2 instead of 0.02. This resulted in the coverage filter not being as stringent as it should’ve been.
- There were a number of bugs in pVACapi and pVACviz that would prevent a user from submitting jobs using the interface in certain conditions. These have been resolved.
- pVACseq would previsouly not support SVs in the input VCF where the alt had
a value of
<DEL>. These kinds of variants are now supported.