After pVACvector is run and a successful solution is created, a review document is generated. This includes the text from the pVACvector fasta output but with the neoantigen candidate colored, mutation positions underlined, and class ii candidate in bold. This is similar to the "CANDIDATE NEOANTIGEN AMINO ACID SEQUENCE WITH FLANKING RESIDUES" column in the peptide ordering spreadsheet but seems to be a manual process.
We should add a new command under the pvacvector command tree that takes in the pvacvector output fasta, the aggregated report, and any other required files and generates a TXT/DOC version of the fasta file but with the formatting applied.
After pVACvector is run and a successful solution is created, a review document is generated. This includes the text from the pVACvector fasta output but with the neoantigen candidate colored, mutation positions underlined, and class ii candidate in bold. This is similar to the "CANDIDATE NEOANTIGEN AMINO ACID SEQUENCE WITH FLANKING RESIDUES" column in the peptide ordering spreadsheet but seems to be a manual process.
We should add a new command under the pvacvector command tree that takes in the pvacvector output fasta, the aggregated report, and any other required files and generates a TXT/DOC version of the fasta file but with the formatting applied.