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UsageΒΆ

Warning

Using a local IEDB installation is strongly recommended for larger datasets or when the making predictions for many alleles, epitope lengths, or prediction algorithms. More information on how to install IEDB locally can be found on the Installation page.

usage: pvacvector run [-h] [-e EPITOPE_LENGTH]
                      [--iedb-install-directory IEDB_INSTALL_DIRECTORY]
                      [-b BINDING_THRESHOLD] [-r IEDB_RETRIES] [-k]
                      [-v INPUT_VCF] [-n INPUT_N_MER]
                      input_file sample_name allele
                      {NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign}
                      [{NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign} ...]
                      output_dir

positional arguments:
  input_file            A .fa file with peptides or a pVACseq .tsv file with
                        eptiopes to use for vector design.
  sample_name           The name of the sample being processed. This will be
                        used as a prefix for output files
  allele                Name of the allele to use for epitope prediction.
                        Multiple alleles can be specified using a comma-
                        separated list. For a list of available alleles, use:
                        `pvacseq valid_alleles`
  {NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign}
                        The epitope prediction algorithms to use. Multiple
                        prediction algorithms can be specified, separated by
                        spaces
  output_dir            The directory for writing all result files

optional arguments:
  -h, --help            show this help message and exit
  -e EPITOPE_LENGTH, --epitope-length EPITOPE_LENGTH
                        Length of subpeptides (neoepitopes) to predict.
                        Multiple epitope lengths can be specified using a
                        comma-separated list. Typical epitope lengths vary
                        between 8-11. Required for Class I prediction
                        algorithms
  --iedb-install-directory IEDB_INSTALL_DIRECTORY
                        Directory that contains the local installation of IEDB
                        MHC I and/or MHC II
  -b BINDING_THRESHOLD, --binding-threshold BINDING_THRESHOLD
                        Report only epitopes where the mutant allele has ic50
                        binding scores below this value. Default: 500
  -r IEDB_RETRIES, --iedb-retries IEDB_RETRIES
                        Number of retries when making requests to the IEDB
                        RESTful web interface. Must be less than or equal to
                        100.Default: 5
  -k, --keep-tmp-files  Keep intermediate output files. This migt be useful
                        for debugging purposes.
  -v INPUT_VCF, --input_vcf INPUT_VCF
                        Path to original pVACseq input VCF file. Required if
                        input file is a pVACseq TSV.
  -n INPUT_N_MER, --input-n-mer INPUT_N_MER
                        Length of the peptide sequence to use when creating
                        the FASTA from the pVACseq TSV. Default: 21