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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]
                    [--allele-specific-binding-thresholds]
                    [-m {lowest,median}] [-r IEDB_RETRIES] [-k] [-t N_THREADS]
                    [-l PEPTIDE_SEQUENCE_LENGTH]
                    [--normal-sample-name NORMAL_SAMPLE_NAME]
                    [--net-chop-method {cterm,20s}] [--netmhc-stab]
                    [--net-chop-threshold NET_CHOP_THRESHOLD]
                    [-a {sample_name}] [-s FASTA_SIZE]
                    [-d DOWNSTREAM_SEQUENCE_LENGTH] [--exclude-NAs]
                    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            An INTEGRATE-Neo annotated 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`.
  {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 `pvacfuse
                        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)
  -l PEPTIDE_SEQUENCE_LENGTH, --peptide-sequence-length PEPTIDE_SEQUENCE_LENGTH
                        Length of the peptide sequence to use when creating
                        the FASTA. (default: 21)
  --normal-sample-name NORMAL_SAMPLE_NAME
                        In a multi-sample VCF, the name of the matched normal
                        sample. (default: None)
  --net-chop-method {cterm,20s}
                        NetChop prediction method to use ("cterm" for C term
                        3.0, "20s" for 20S 3.0). C-term 3.0 is trained with
                        publicly available MHC class I ligands and the authors
                        believe that is performs best in predicting the
                        boundaries of CTL epitopes. 20S is trained with in
                        vitro degradation data. (default: None)
  --netmhc-stab         Run NetMHCStabPan after all filtering and add
                        stability predictions to predicted epitopes. (default:
                        False)
  --net-chop-threshold NET_CHOP_THRESHOLD
                        NetChop prediction threshold (increasing the threshold
                        results in better specificity, but worse sensitivity).
                        (default: 0.5)
  -a {sample_name}, --additional-report-columns {sample_name}
                        Additional columns to output in the final report. If
                        sample_name is chosen, this will add a column with the
                        sample name in every row of the output. This can be
                        useful if you later want to concatenate results from
                        multiple individuals into a single file. (default:
                        None)
  -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)