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.
Creating converter from 7 to 5
Creating converter from 5 to 7
Creating converter from 7 to 5
Creating converter from 5 to 7
usage: pvacfuse run [-h] [--iedb-install-directory IEDB_INSTALL_DIRECTORY]
[-r IEDB_RETRIES] [-k] [-t N_THREADS]
[--netmhciipan-version {4.3,4.2,4.1,4.0}]
[--use-normalized-percentiles]
[--reference-scores-path REFERENCE_SCORES_PATH]
[-e1 CLASS_I_EPITOPE_LENGTH] [-e2 CLASS_II_EPITOPE_LENGTH]
[-b BINDING_THRESHOLD]
[--binding-percentile-threshold BINDING_PERCENTILE_THRESHOLD]
[--immunogenicity-percentile-threshold IMMUNOGENICITY_PERCENTILE_THRESHOLD]
[--presentation-percentile-threshold PRESENTATION_PERCENTILE_THRESHOLD]
[--percentile-threshold-strategy {conservative,exploratory}]
[--allele-specific-binding-thresholds]
[-m {lowest,median}] [-m2 TOP_SCORE_METRIC2]
[--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] [-d DOWNSTREAM_SEQUENCE_LENGTH]
[--genes-of-interest-file GENES_OF_INTEREST_FILE]
[--aggregate-inclusion-binding-threshold AGGREGATE_INCLUSION_BINDING_THRESHOLD]
[--aggregate-inclusion-count-limit AGGREGATE_INCLUSION_COUNT_LIMIT]
[--starfusion-file STARFUSION_FILE]
[--read-support READ_SUPPORT] [--expn-val EXPN_VAL]
input_file sample_name allele
{BigMHC_EL,BigMHC_IM,DeepImmuno,MHCflurry,MHCflurryEL,MHCnuggetsI,MHCnuggetsII,MixMHCpred,NNalign,NetMHC,NetMHCIIpan,NetMHCIIpanEL,NetMHCcons,NetMHCpan,NetMHCpanEL,PRIME,PickPocket,SMM,SMMPMBEC,SMMalign,all,all_class_i,all_class_ii}
[{BigMHC_EL,BigMHC_IM,DeepImmuno,MHCflurry,MHCflurryEL,MHCnuggetsI,MHCnuggetsII,MixMHCpred,NNalign,NetMHC,NetMHCIIpan,NetMHCIIpanEL,NetMHCcons,NetMHCpan,NetMHCpanEL,PRIME,PickPocket,SMM,SMMPMBEC,SMMalign,all,all_class_i,all_class_ii} ...]
output_dir
Run the pVACfuse pipeline
positional arguments:
input_file An AGFusion output directory or Arriba fusion.tsv
output file.
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:
`pvacfuse valid_alleles`.
{BigMHC_EL,BigMHC_IM,DeepImmuno,MHCflurry,MHCflurryEL,MHCnuggetsI,MHCnuggetsII,MixMHCpred,NNalign,NetMHC,NetMHCIIpan,NetMHCIIpanEL,NetMHCcons,NetMHCpan,NetMHCpanEL,PRIME,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
--iedb-install-directory IEDB_INSTALL_DIRECTORY
Directory that contains the local installation of IEDB
MHC I and/or MHC II. (default: None)
-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)
--netmhciipan-version {4.3,4.2,4.1,4.0}
Specify the version of NetMHCIIpan or NetMHCIIpanEL to
be used during the run. (default: 4.1)
--use-normalized-percentiles
When set, calculate normalized percentile scores for
all prediction algorithms. For algorithms that do not
natively provide percentiles, percentiles will be
derived by comparing prediction scores against pre-
computed reference distributions. For algorithms that
do provide native percentiles, their values will be
overwritten with the normalized percentile. (default:
False)
--reference-scores-path REFERENCE_SCORES_PATH
Directory to store pre-computed reference percentile
files. If a file is missing, it will be downloaded
here when --use-normalized-percentiles is set.
(default: /tmp)
-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])
-b BINDING_THRESHOLD, --binding-threshold BINDING_THRESHOLD
Report only epitopes where the mutant allele has ic50
binding scores below this value. (default: 500)
--binding-percentile-threshold BINDING_PERCENTILE_THRESHOLD
Report only epitopes where the mutant allele has a
binding percentile rank below this value. (default:
2.0)
--immunogenicity-percentile-threshold IMMUNOGENICITY_PERCENTILE_THRESHOLD
Report only epitopes where the mutant allele has a
immunogenicity percentile rank below this value.
(default: 2.0)
--presentation-percentile-threshold PRESENTATION_PERCENTILE_THRESHOLD
Report only epitopes where the mutant allele has a
presentation percentile rank below this value.
(default: 2.0)
--percentile-threshold-strategy {conservative,exploratory}
Specify the candidate inclusion strategy. The
'conservative' option requires a candidate to pass
BOTH the binding threshold and all percentile
thresholds set (default). The 'exploratory' option
requires a candidate to pass EITHER the binding
threshold or any of the percentile thresholds set.
(default: conservative)
--allele-specific-binding-thresholds
Use allele-specific binding thresholds. To print the
allele-specific binding thresholds run `pvacfuse
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)
-m2 TOP_SCORE_METRIC2, --top-score-metric2 TOP_SCORE_METRIC2
Which metrics to consider when selecting the best
peptide in the aggregate erport and the top score
filter step (filtered report). Each specified metric
will be ranked and the sum of these ranks will be
used. This rank sum is also used as the primary
sorting criteria in the aggregated report for the
candidates within each tier as well as in the filtered
report. Whether the lowest or median is considered for
each metric is controlled by the --top-score-metric
parameter. (default: ['ic50', 'combined_percentile'])
--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)
-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)
--genes-of-interest-file GENES_OF_INTEREST_FILE
A genes of interest file. Predictions resulting from
variants on genes in this list will be marked in the
result files. The file should be formatted to have
each gene on a separate line without a header line. If
no file is specified, the Cancer Gene Census list of
high-confidence genes is used as the default.
(default: None)
--aggregate-inclusion-binding-threshold AGGREGATE_INCLUSION_BINDING_THRESHOLD
Threshold for including epitopes when creating the
aggregate report (default: 5000)
--aggregate-inclusion-count-limit AGGREGATE_INCLUSION_COUNT_LIMIT
Limit neoantigen candidates included in the aggregate
report to only the best n candidates per variant.
(default: 15)
--starfusion-file STARFUSION_FILE
Path to a star-fusion.fusion_predictions.tsv or star-
fusion.fusion_predictions.abridged.tsv to extract read
support and expression information from. When running
with AGFusion data, both read support and expression
data from this file will be used. When running with
Arriba data, only expression data from this file is
used while read support data will be parsed from the
Arriba data directly. (default: None)
--read-support READ_SUPPORT
Read Support Cutoff. Sites above this cutoff will be
considered. (default: 5)
--expn-val EXPN_VAL Expression Cutoff. Expression is meassured as FFPM
(fusion fragments per million total reads). Sites
above this cutoff will be considered. (default: 0.1)