Getting Started

pVACfuse provides a set of example data to show the expected format of input and output files. You can download the data set by running the pvacfuse download_example_data command.

There are two option as to how to run pVACfuse. It accepts either a INTEGRATE-neo output bedpe file or a AGFusion output directory.

The following command is an example for how to run pVACfuse with an INTEGRATE-neo bedpe file and will regenerate the results_from_integrate_neo example data:

pvacfuse run \
<example_data_dir>/fusions.bedpe.annot \
Test \
HLA-A*02:01,HLA-B*35:01,DRB1*11:01 \
MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign \
<output_dir> \
-e1 8,9,10 \
-e2 15

The results_from_agfusion example data can be regenerated like so:

pvacfuse run \
<example_data_dir>/agfusion/ \
Test \
HLA-A*02:01,HLA-B*35:01,DRB1*11:01 \
MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign \
<output_dir> \
-e1 8,9,10 \
-e2 15

A detailed description of all command options can be found on the Usage page.