UsageΒΆ

usage: pvacseq run [-h] [-e EPITOPE_LENGTH] [-l PEPTIDE_SEQUENCE_LENGTH]
                   [--iedb-install-directory IEDB_INSTALL_DIRECTORY]
                   [-i ADDITIONAL_INPUT_FILE_LIST]
                   [--net-chop-method {cterm,20s}] [--netmhc-stab] [-t]
                   [-m {lowest,median}] [-b BINDING_THRESHOLD]
                   [-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]
                   [--net-chop-threshold NET_CHOP_THRESHOLD] [-s FASTA_SIZE]
                   [-r IEDB_RETRIES] [-d DOWNSTREAM_SEQUENCE_LENGTH] [-k]
                   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
Required 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 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`
prediction_algorithms
 

The epitope prediction algorithms to use. Multiple prediction algorithms can be specified, separated by spaces

Possible choices: NNalign, NetMHC, NetMHCIIpan, NetMHCcons, NetMHCpan, PickPocket, SMM, SMMPMBEC, SMMalign

output_dir The directory for writing all result files
Optional Arguments
-e, --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
-l=21, --peptide-sequence-length=21
 Length of the peptide sequence to use when creating the FASTA. Default: 21
--iedb-install-directory
 Directory that contains the local installation of IEDB MHC I and/or MHC II
-i, --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`.
--net-chop-method
 

NetChop prediction method to use (“cterm” for C term 3.0, “20s” for 20S 3.0).

Possible choices: cterm, 20s

--netmhc-stab=False
 Run NetMHCStabPan after all filtering and add stability predictions to predicted epitopes
-t=False, --top-result-per-mutation=False
 Output only the top scoring result for each allele-peptide length combination for each variant. Default: False
-m="median", --top-score-metric="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

Possible choices: lowest, median

-b=500, --binding-threshold=500
 Report only epitopes where the mutant allele has ic50 binding scores below this value. Default: 500
-c=0, --minimum-fold-change=0
 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=5 Normal Coverage Cutoff. Sites above this cutoff will be considered. Default: 5
--tdna-cov=10 Tumor DNA Coverage Cutoff. Sites above this cutoff will be considered. Default: 10
--trna-cov=10 Tumor RNA Coverage Cutoff. Sites above this cutoff will be considered. Default: 10
--normal-vaf=2 Normal VAF Cutoff. Sites BELOW this cutoff in normal will be considered. Default: 2
--tdna-vaf=40 Tumor DNA VAF Cutoff. Sites above this cutoff will be considered. Default: 40
--trna-vaf=40 Tumor RNA VAF Cutoff. Sites above this cutoff will be considered. Default: 40
--expn-val=1 Gene and Transcript Expression cutoff. Sites above this cutoff will be considered. Default: 1
--net-chop-threshold=0.5
 NetChop prediction threshold. Default: 0.5
-s=200, --fasta-size=200
 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.
-r=5, --iedb-retries=5
 Number of retries when making requests to the IEDB RESTful web interface. Must be less than or equal to 100.Default: 5
-d="1000", --downstream-sequence-length="1000"
 Cap to limit the downstream sequence length for frameshifts when creating the fasta file. Use ‘full’ to include the full downstream sequence. Default: 1000
-k=False, --keep-tmp-files=False
 Keep intermediate output files. This migt be useful for debugging purposes.