There are two options for the input file when running the pVACvector tool:
- A fasta file. This file contains protein sequences of candidate neoeptiopes to use for vector design.
- A pVACseq output TSV. This file has been filtered to include
only the neoepitopes to use for vector design. If this file type is
used, it is also necessary to provide the original VCF used in the
pVACseq run via the
--input_vcfoption. Output TSVs from MHC Class I and Class II pVACseq results can be combined into one by concatenating the two files and removing the duplicate header line.