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There are two options for the input file when running the pVACvector tool:

  • A FASTA file. This file contains protein sequences of candidate neoepitopes 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_vcf option. 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.

Note that if you supply a FASTA file of peptides, these peptides will be used directly in the analysis and used in the final output. However, if you use a pvacseq TSV and variants VCF then the length of peptides extracted for junctional epitope testing and reporting in your output will be determined by the --input-n-mer option.