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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]
                      [--allele-specific-binding-thresholds]
                      [-m {lowest,median}] [-r IEDB_RETRIES] [-k]
                      [-t N_THREADS] [-v INPUT_VCF] [-n INPUT_N_MER]
                      [--spacers SPACERS]
                      input_file sample_name allele
                      {MHCflurry,MHCnuggetsI,MHCnuggetsII,NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign}
                      [{MHCflurry,MHCnuggetsI,MHCnuggetsII,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
                        epitopes 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`.
  {MHCflurry,MHCnuggetsI,MHCnuggetsII,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. (default: None)
  --iedb-install-directory IEDB_INSTALL_DIRECTORY
                        Directory that contains the local installation of IEDB
                        MHC I and/or MHC II. (default: None)
  -b BINDING_THRESHOLD, --binding-threshold BINDING_THRESHOLD
                        Report only epitopes where the mutant allele has ic50
                        binding scores below this value. (default: 500)
  --allele-specific-binding-thresholds
                        Use allele-specific binding thresholds. To print the
                        allele-specific binding thresholds run `pvacvector
                        allele_specific_cutoffs`. If an allele does not have a
                        special threshold value, the `--binding-threshold`
                        value will be used. (default: False)
  -m {lowest,median}, --top-score-metric {lowest,median}
                        The ic50 scoring metric to use when filtering epitopes
                        by binding-threshold or minimum fold change. lowest:
                        Use the best MT Score and Corresponding Fold Change
                        (i.e. the lowest MT ic50 binding score and
                        corresponding fold change of all chosen prediction
                        methods). median: Use the median MT Score and Median
                        Fold Change (i.e. the median MT ic50 binding score and
                        fold change of all chosen prediction methods).
                        (default: median)
  -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 might be useful
                        for debugging purposes. (default: False)
  -t N_THREADS, --n-threads N_THREADS
                        Number of threads to use for parallelizing peptide-MHC
                        binding prediction calls. (default: 1)
  -v INPUT_VCF, --input_vcf INPUT_VCF
                        Path to original pVACseq input VCF file. Required if
                        input file is a pVACseq TSV. (default: None)
  -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: 25)
  --spacers SPACERS     Comma-separated list of spacers to use for testing
                        junction epitopes. Include None to test junctions
                        without spacers. (default:
                        None,HH,HHC,HHH,HHHD,HHHC,AAY,HHHH,HHAA,HHL,AAL)