Version 1.3

1.3.0

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 --spacers parameter with a comma-separated list of spacer peptides. Including the string None will also test each junction without spacers. The default is None,HH,HHC,HHH,HHHD,HHHC,AAY,HHHH,HHAA,HHL,AAL
  • The --expn-val cutoff 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:

  • The --normal-vaf cutoff 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.