pVACseq logo

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] [-e1 CLASS_I_EPITOPE_LENGTH]
                   [-e2 CLASS_II_EPITOPE_LENGTH]
                   [--iedb-install-directory IEDB_INSTALL_DIRECTORY]
                   [-b BINDING_THRESHOLD]
                   [--percentile-threshold PERCENTILE_THRESHOLD]
                   [--allele-specific-binding-thresholds] [-m {lowest,median}]
                   [-r IEDB_RETRIES] [-k] [-t N_THREADS]
                   [--net-chop-method {cterm,20s}] [--netmhc-stab]
                   [--net-chop-threshold NET_CHOP_THRESHOLD]
                   [--run-reference-proteome-similarity]
                   [--blastp-path BLASTP_PATH]
                   [--blastp-db {refseq_select_prot,refseq_protein}]
                   [-a {sample_name}] [-s FASTA_SIZE] [--exclude-NAs]
                   [-d DOWNSTREAM_SEQUENCE_LENGTH]
                   [--normal-sample-name NORMAL_SAMPLE_NAME]
                   [-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] [--tumor-purity TUMOR_PURITY]
                   input_file sample_name allele
                   {MHCflurry,MHCnuggetsI,MHCnuggetsII,NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign,all,all_class_i,all_class_ii}
                   [{MHCflurry,MHCnuggetsI,MHCnuggetsII,NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign,all,all_class_i,all_class_ii} ...]
                   output_dir

Run the pVACseq pipeline

positional arguments:
  input_file            A VEP-annotated single- or multi-sample VCF containing
                        genotype, transcript, Wildtype protein sequence, and
                        Downstream protein sequence information.The VCF may be
                        gzipped (requires tabix index).
  sample_name           The name of the tumor sample being processed. When
                        processing a multi-sample VCF the sample name must be
                        a sample ID in the input VCF #CHROM header line.
  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,all,all_class_i,all_class_ii}
                        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
  -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)
  -b BINDING_THRESHOLD, --binding-threshold BINDING_THRESHOLD
                        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)
  --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)
  -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)
  --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)
  --run-reference-proteome-similarity
                        Blast peptides against the reference proteome.
                        (default: False)
  --blastp-path BLASTP_PATH
                        Blastp installation path. (default: None)
  --blastp-db {refseq_select_prot,refseq_protein}
                        The blastp database to use. (default:
                        refseq_select_prot)
  -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)
  --exclude-NAs         Exclude NA values from the filtered output. (default:
                        False)
  -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)
  --normal-sample-name NORMAL_SAMPLE_NAME
                        In a multi-sample VCF, the name of the matched normal
                        sample. (default: None)
  -p PHASED_PROXIMAL_VARIANTS_VCF, --phased-proximal-variants-vcf PHASED_PROXIMAL_VARIANTS_VCF
                        A VCF with phased proximal variant information. Must
                        be gzipped and tabix indexed. (default: None)
  -c MINIMUM_FOLD_CHANGE, --minimum-fold-change MINIMUM_FOLD_CHANGE
                        Minimum fold change between mutant (MT) binding score
                        and wild-type (WT) score (fold change = WT/MT). 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 peptide). This fold change is sometimes
                        referred to as a differential agretopicity index.
                        (default: 0.0)
  --normal-cov NORMAL_COV
                        Normal Coverage Cutoff. Only sites above this read
                        depth cutoff will be considered. (default: 5)
  --tdna-cov TDNA_COV   Tumor DNA Coverage Cutoff. Only sites above this read
                        depth cutoff will be considered. (default: 10)
  --trna-cov TRNA_COV   Tumor RNA Coverage Cutoff. Only sites above this read
                        depth cutoff will be considered. (default: 10)
  --normal-vaf NORMAL_VAF
                        Normal VAF Cutoff. Only sites BELOW this cutoff in
                        normal will be considered. (default: 0.02)
  --tdna-vaf TDNA_VAF   Tumor DNA VAF Cutoff. Only sites above this cutoff
                        will be considered. (default: 0.25)
  --trna-vaf TRNA_VAF   Tumor RNA VAF Cutoff. Only sites above this cutoff
                        will be considered. (default: 0.25)
  --expn-val EXPN_VAL   Gene and Transcript Expression cutoff. Only sites
                        above this cutoff will be considered. (default: 1.0)
  --maximum-transcript-support-level {1,2,3,4,5}
                        The threshold to use for filtering epitopes on the
                        Ensembl transcript support level (TSL). Keep all
                        epitopes with a transcript support level <= to this
                        cutoff. (default: 1)
  --pass-only           Only process VCF entries with a PASS status. (default:
                        False)
  --tumor-purity TUMOR_PURITY
                        Value between 0 and 1 indicating the fraction of tumor
                        cells in the tumor sample. Information is used during
                        aggregate report creation for a simple estimation of
                        whether variants are subclonal or clonal based on VAF.
                        If not provided, purity is estimated directly from the
                        VAFs. (default: None)