Usage

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] [-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.