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]
[--aggregate-inclusion-binding-threshold AGGREGATE_INCLUSION_BINDING_THRESHOLD]
[-m {lowest,median}] [-r IEDB_RETRIES] [-k] [-t N_THREADS]
[--net-chop-method {cterm,20s}] [--netmhc-stab]
[--net-chop-threshold NET_CHOP_THRESHOLD]
[--problematic-amino-acids PROBLEMATIC_AMINO_ACIDS]
[--run-reference-proteome-similarity]
[--blastp-path BLASTP_PATH]
[--blastp-db {refseq_select_prot,refseq_protein}]
[--peptide-fasta PEPTIDE_FASTA] [-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}]
[--allele-specific-anchors]
[--anchor-contribution-threshold ANCHOR_CONTRIBUTION_THRESHOLD]
[--pass-only] [--tumor-purity TUMOR_PURITY]
input_file sample_name allele
{MHCflurry,MHCflurryEL,MHCnuggetsI,MHCnuggetsII,NNalign,NetMHC,NetMHCIIpan,NetMHCIIpanEL,NetMHCcons,NetMHCpan,NetMHCpanEL,PickPocket,SMM,SMMPMBEC,SMMalign,all,all_class_i,all_class_ii}
[{MHCflurry,MHCflurryEL,MHCnuggetsI,MHCnuggetsII,NNalign,NetMHC,NetMHCIIpan,NetMHCIIpanEL,NetMHCcons,NetMHCpan,NetMHCpanEL,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
Frameshift 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,MHCflurryEL,MHCnuggetsI,MHCnuggetsII,NNalign,NetMHC,NetMHCIIpan,NetMHCIIpanEL,NetMHCcons,NetMHCpan,NetMHCpanEL,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)
--aggregate-inclusion-binding-threshold AGGREGATE_INCLUSION_BINDING_THRESHOLD
Threshold for including epitopes when creating the
aggregate report (default: 5000)
-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)
--problematic-amino-acids PROBLEMATIC_AMINO_ACIDS
A list of amino acids to consider as problematic. Each
entry can be specified in the following format:
`amino_acid(s)`: One or more one-letter amino acid
codes. Any occurrence of this amino acid string,
regardless of the position in the epitope, is
problematic. When specifying more than one amino acid,
they will need to occur together in the specified
order. `amino_acid:position`: A one letter amino acid
code, followed by a colon separator, followed by a
positive integer position (one-based). The occurrence
of this amino acid at the position specified is
problematic., E.g. G:2 would check for a Glycine at
the second position of the epitope. The N-terminus is
defined as position 1. `amino_acid:-position`: A one
letter amino acid code, followed by a colon separator,
followed by a negative integer position. The
occurrence of this amino acid at the specified
position from the end of the epitope is problematic.
E.g., G:-3 would check for a Glycine at the third
position from the end of the epitope. The C-terminus
is defined as position -1. (default: None)
--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)
--peptide-fasta PEPTIDE_FASTA
When running the reference proteome similarity step,
use this reference peptide FASTA file to find matches
instead of blastp. (default: None)
-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)
--allele-specific-anchors
Use allele-specific anchor positions when tiering
epitopes in the aggregate report. This option is
available for 8, 9, 10, and 11mers and only for HLA-A,
B, and C alleles. If this option is not enabled or as
a fallback for unsupported lengths and alleles, the
default positions of 1, 2, epitope length - 1, and
epitope length are used. Please see
https://doi.org/10.1101/2020.12.08.416271 for more
details. (default: False)
--anchor-contribution-threshold ANCHOR_CONTRIBUTION_THRESHOLD
For determining allele-specific anchors, each position
is assigned a score based on how binding is influenced
by mutations. From these scores, the relative
contribution of each position to the overall binding
is calculated. Starting with the highest relative
contribution, positions whose scores together account
for the selected contribution threshold are assigned
as anchor locations. As a result, a higher threshold
leads to the inclusion of more positions to be
considered anchors. (default: 0.8)
--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)