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 in decimal format. Only sites BELOW
this cutoff in normal will be considered. (default:
0.02)
--tdna-vaf TDNA_VAF Tumor DNA VAF Cutoff in decimal format. Only sites
above this cutoff will be considered. (default: 0.25)
--trna-vaf TRNA_VAF Tumor RNA VAF Cutoff in decimal format. 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)