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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: pvacfuse run [-h] [-e EPITOPE_LENGTH]
                    [--iedb-install-directory IEDB_INSTALL_DIRECTORY]
                    [-b BINDING_THRESHOLD] [-r IEDB_RETRIES] [-k]
                    [-l PEPTIDE_SEQUENCE_LENGTH]
                    [--net-chop-method {cterm,20s}] [--netmhc-stab] [-t]
                    [-m {lowest,median}]
                    [--net-chop-threshold NET_CHOP_THRESHOLD]
                    [-a {sample_name}] [-s FASTA_SIZE]
                    [-d DOWNSTREAM_SEQUENCE_LENGTH] [--exclude-NAs]
                    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 INTEGRATE-Neo bedpe file with fusions.
  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.
  -l PEPTIDE_SEQUENCE_LENGTH, --peptide-sequence-length PEPTIDE_SEQUENCE_LENGTH
                        Length of the peptide sequence to use when creating
                        the FASTA. Default: 21
  --net-chop-method {cterm,20s}
                        NetChop prediction method to use ("cterm" for C term
                        3.0, "20s" for 20S 3.0).
  --netmhc-stab         Run NetMHCStabPan after all filtering and add
                        stability predictions to predicted epitopes
  -t, --top-result-per-mutation
                        Output only the top scoring result for each allele-
                        peptide length combination for each variant. 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:
                        Best MT Score/Corresponding Fold Change - lowest MT
                        ic50 binding score/corresponding fold change of all
                        chosen prediction methods. median: Median MT
                        Score/Median Fold Change - median MT ic50 binding
                        score/fold change of all chosen prediction methods.
                        Default: median
  --net-chop-threshold NET_CHOP_THRESHOLD
                        NetChop prediction threshold. Default: 0.5
  -a {sample_name}, --additional-report-columns {sample_name}
                        Additional columns to output in the final report
  -s FASTA_SIZE, --fasta-size FASTA_SIZE
                        Number of fasta entries per IEDB request. For some
                        resource-intensive prediction algorithms like
                        Pickpocket and NetMHCpan it might be helpful to reduce
                        this number. Needs to be an even number. Default: 200
  -d DOWNSTREAM_SEQUENCE_LENGTH, --downstream-sequence-length DOWNSTREAM_SEQUENCE_LENGTH
                        Cap to limit the downstream sequence length for
                        frameshifts when creating the fasta file. Use 'full'
                        to include the full downstream sequence. Default: 1000
  --exclude-NAs         Exclude NA values from the filtered output. Default:
                        False