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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: pvacseq run [-h] [-e EPITOPE_LENGTH]
                   [--iedb-install-directory IEDB_INSTALL_DIRECTORY]
                   [-b BINDING_THRESHOLD]
                   [--allele-specific-binding-thresholds] [-r IEDB_RETRIES]
                   [-k] [-l PEPTIDE_SEQUENCE_LENGTH]
                   [--normal-sample-name NORMAL_SAMPLE_NAME]
                   [--net-chop-method {cterm,20s}] [--netmhc-stab]
                   [-m {lowest,median}]
                   [--net-chop-threshold NET_CHOP_THRESHOLD]
                   [-a {sample_name}] [-s FASTA_SIZE]
                   [-d DOWNSTREAM_SEQUENCE_LENGTH] [--exclude-NAs]
                   [-i ADDITIONAL_INPUT_FILE_LIST]
                   [-p PHASED_PROXIMAL_VARIANTS_VCF] [-c MINIMUM_FOLD_CHANGE]
                   [--normal-cov NORMAL_COV] [--tdna-cov TDNA_COV]
                   [--trna-cov TRNA_COV] [--normal-vaf NORMAL_VAF]
                   [--tdna-vaf TDNA_VAF] [--trna-vaf TRNA_VAF]
                   [--expn-val EXPN_VAL]
                   [--maximum-transcript-support-level {1,2,3,4,5}]
                   [--pass-only]
                   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 VEP-annotated single-sample VCF containing
                        transcript, Wildtype protein sequence, and Downstream
                        protein sequence information.
  sample_name           The name of the tumor sample being processed. Must be
                        a sample in the input VCF.
  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
  --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
  --allele-specific-binding-thresholds
                        Use allele-specific binding thresholds. To print the
                        allele-specific binding thresholds run `pvacseq
                        allele_specific_cutoffs`. If an allele does not have a
                        special threshold value, the `--binding-threshold`
                        value will be used. Default: False
  -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
  --normal-sample-name NORMAL_SAMPLE_NAME
                        In a multi-sample VCF, the name of the matched normal
                        sample.
  --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
  -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
  -i ADDITIONAL_INPUT_FILE_LIST, --additional-input-file-list ADDITIONAL_INPUT_FILE_LIST
                        yaml file of additional files to be used as inputs,
                        e.g. cufflinks output files. For an example of this
                        yaml file run `pvacseq config_files
                        additional_input_file_list`.
  -p PHASED_PROXIMAL_VARIANTS_VCF, --phased-proximal-variants-vcf PHASED_PROXIMAL_VARIANTS_VCF
                        A VCF with phased proximal variant information
  -c MINIMUM_FOLD_CHANGE, --minimum-fold-change MINIMUM_FOLD_CHANGE
                        Minimum fold change between mutant binding score and
                        wild-type score. The default is 0, which filters no
                        results, but 1 is often a sensible choice (requiring
                        that binding is better to the MT than WT). Default: 0
  --normal-cov NORMAL_COV
                        Normal Coverage Cutoff. Sites above this cutoff will
                        be considered. Default: 5
  --tdna-cov TDNA_COV   Tumor DNA Coverage Cutoff. Sites above this cutoff
                        will be considered. Default: 10
  --trna-cov TRNA_COV   Tumor RNA Coverage Cutoff. Sites above this cutoff
                        will be considered. Default: 10
  --normal-vaf NORMAL_VAF
                        Normal VAF Cutoff. Sites BELOW this cutoff in normal
                        will be considered. Default: 0.02
  --tdna-vaf TDNA_VAF   Tumor DNA VAF Cutoff. Sites above this cutoff will be
                        considered. Default: 0.25
  --trna-vaf TRNA_VAF   Tumor RNA VAF Cutoff. Sites above this cutoff will be
                        considered. Default: 0.25
  --expn-val EXPN_VAL   Gene and Transcript Expression cutoff. Sites above
                        this cutoff will be considered. Default: 1
  --maximum-transcript-support-level {1,2,3,4,5}
                        The threshold to use for filtering epitopes on the
                        transcript support level. Keep all epitopes with a
                        transcript support level <= to this cutoff. Default: 1
  --pass-only           Only process VCF entries that are PASS. Default: False
Using TensorFlow backend.
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