Optional Downstream Analysis Tools

Generate Protein Fasta

usage: pvacfuse [-h]
                {run,binding_filter,top_score_filter,generate_protein_fasta,valid_alleles,allele_specific_cutoffs,download_example_data}
                ...

positional arguments:
  {run,binding_filter,top_score_filter,generate_protein_fasta,valid_alleles,allele_specific_cutoffs,download_example_data}
    run                 Runs the pVACfuse pipeline
    binding_filter      Filters variants processed by IEDB by binding score
    top_score_filter    Pick the best neoepitope for each variant
    generate_protein_fasta
                        Generate an annotated fasta file from Integrate-Neo or
                        AGFusion output
    valid_alleles       Shows a list of valid allele names
    allele_specific_cutoffs
                        Show the allele specific cutoffs
    download_example_data
                        Downloads example input and output files

optional arguments:
  -h, --help            show this help message and exit
Error: No command specified

This tool will extract protein sequences surrounding fusion variant in an by parsing Integrate-Neo or AGFusion output. One use case for this tool is to help select long peptides that contain short neoepitope candidates. For example, if pvacfuse was run to predict nonamers (9-mers) that are good binders and the user wishes to select long peptide (e.g. 24-mer) sequences that contain the nonamer for synthesis or encoding in a DNA vector. The fusion position will be centered in the protein sequence returned (if possible). If the fusion causes a frameshift, the full downstream protein sequence will be returned unless the user specifies otherwise as described above.