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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.

It may be necessary to explore the parameter space a bit when running pVACvector. As binding predictions for some sites vary substantially across algorithms, the most conservative settings may result in no valid paths, often due to one “outlier” prediction. Carefully choosing which predictors to run may help ameliorate this issue as well.

In general, setting a lower binding threshold (e.g., 500nM) and using the median binding value (--top-score-metric median) will lead to greater possibility of a design, while more conservative settings of 1000nM and lowest/best binding value (--top-score-metric lowest) will give more confidence that there are no junctional neoepitopes.

Our current recommendation is to run pVACvector several different ways, and choose the path resulting from the most conservative set of parameters.

usage: pvacvector run [-h] [-e1 CLASS_I_EPITOPE_LENGTH]
                      [-e2 CLASS_II_EPITOPE_LENGTH]
                      [--iedb-install-directory IEDB_INSTALL_DIRECTORY]
                      [-b BINDING_THRESHOLD]
                      [--percentile-threshold PERCENTILE_THRESHOLD]
                      [--aggregate-inclusion-binding-threshold AGGREGATE_INCLUSION_BINDING_THRESHOLD]
                      [-m {lowest,median}] [-r IEDB_RETRIES] [-k]
                      [-t N_THREADS] [-v INPUT_VCF] [-n INPUT_N_MER]
                      [--spacers SPACERS] [--max-clip-length MAX_CLIP_LENGTH]
                      input_file sample_name allele
                      [{MHCflurry,MHCflurryEL,MHCnuggetsI,MHCnuggetsII,NNalign,NetMHC,NetMHCIIpan,NetMHCIIpanEL,NetMHCcons,NetMHCpan,NetMHCpanEL,PickPocket,SMM,SMMPMBEC,SMMalign,all,all_class_i,all_class_ii} ...]

Run the pVACvector pipeline

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:
                        `pvacvector valid_alleles`.
                        The epitope prediction algorithms to use. Multiple
                        prediction algorithms can be specified, separated by
  output_dir            The directory for writing all result files.

optional arguments:
  -h, --help            show this help message and exit
  -e1 CLASS_I_EPITOPE_LENGTH, --class-i-epitope-length CLASS_I_EPITOPE_LENGTH
                        Length of MHC Class I subpeptides (neoepitopes) to
                        predict. Multiple epitope lengths can be specified
                        using a comma-separated list. Typical epitope lengths
                        vary between 8-15. Required for Class I prediction
                        algorithms. (default: [8, 9, 10, 11])
  -e2 CLASS_II_EPITOPE_LENGTH, --class-ii-epitope-length CLASS_II_EPITOPE_LENGTH
                        Length of MHC Class II subpeptides (neoepitopes) to
                        predict. Multiple epitope lengths can be specified
                        using a comma-separated list. Typical epitope lengths
                        vary between 11-30. Required for Class II prediction
                        algorithms. (default: [12, 13, 14, 15, 16, 17, 18])
  --iedb-install-directory IEDB_INSTALL_DIRECTORY
                        Directory that contains the local installation of IEDB
                        MHC I and/or MHC II. (default: None)
                        Report only epitopes where the mutant allele has ic50
                        binding scores below this value. (default: 500)
  --percentile-threshold PERCENTILE_THRESHOLD
                        Report only epitopes where the mutant allele has a
                        percentile rank below this value. (default: None)
                        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)
  --aggregate-inclusion-binding-threshold AGGREGATE_INCLUSION_BINDING_THRESHOLD
                        Threshold for including epitopes when creating the
                        aggregate report (default: 5000)
  -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. Peptide combinations will be tested
                        with each spacer in the order specified. (default: Non
  --max-clip-length MAX_CLIP_LENGTH
                        Number of amino acids to permit clipping from the
                        start and/or end of peptides in order to test novel
                        junction epitopes when the first pass on the full
                        peptide fails. (default: 3)