.. image:: images/pVACfuse_logo_trans-bg_sm_v4b.png
    :align: right
    :alt: pVACfuse logo

.. _pvacfuse:

pVACfuse
====================================

This component of the pVACtools workflow provides support for predicting
neoantigens from gene fusions. Currently, fusion variants as reported by
`INTEGRATE-Neo <https://github.com/ChrisMaherLab/INTEGRATE-Neo>`_ are supported, 
and any of the binding affinity prediction software available in pVACseq can 
be used for binding prediction.

.. toctree::
   :glob:

   pvacfuse/prerequisites
   pvacfuse/getting_started
   pvacfuse/run
   pvacfuse/output_files
   pvacfuse/filter_commands
   pvacfuse/additional_commands
   pvacfuse/optional_downstream_analysis_tools