Optional Downstream Analysis Tools¶
Generate Aggregated Report¶
usage: pvacbind generate_aggregated_report [-h] input_file output_file
Generate an aggregated report from a pVACbind .all_epitopes.tsv report file.
positional arguments:
input_file A pVACbind .all_epitopes.tsv report file
output_file The file path to write the aggregated report tsv to
optional arguments:
-h, --help show this help message and exit
This tool produces an aggregated version of the all_epitopes TSV. It finds the best-scoring (lowest binding affinity) epitope for each variant, and outputs additional binding affinity for that epitope. It also gives information about the total number of well-scoring epitopes for each variant, as well as the HLA alleles that those epitopes are well-binding to. For a full overview of the output, see the pVACbind output file documentation.
Calculate Reference Proteome Similarity¶
usage: pvacbind calculate_reference_proteome_similarity [-h]
[--match-length MATCH_LENGTH]
[--species SPECIES]
[--blastp-path BLASTP_PATH]
[--blastp-db {refseq_select_prot,refseq_protein}]
[-t N_THREADS]
input_file input_fasta
output_file
Blast peptides against the reference proteome.
positional arguments:
input_file Input filtered or all_epitopes file with predicted
epitopes.
input_fasta For pVACbind, the original input FASTA file. For
pVACseq and pVACfuse a FASTA file with mutant peptide
sequences for each variant isoform. This file can be
found in the same directory as the input
filtered/all_epitopes file. Can also be generated by
running `pvacseq|pvacfuse generate_protein_fasta`.
output_file Output TSV filename for putative neoepitopes.
optional arguments:
-h, --help show this help message and exit
--match-length MATCH_LENGTH
The desired matching epitope length. (default: 8)
--species SPECIES The species of the input file. (default: human)
--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)
-t N_THREADS, --n-threads N_THREADS
Number of threads to use for parallelizing BLAST
calls. (default: 1)
This tool will Blast peptides against the relative reference proteome and return the results in an output TSV & reference_match file pair, given a pVACbind run’s fasta and filtered/all_epitopes TSV. Typically, this can be done as part of the pVACbind run pipeline for the filtered output TSV if specified. This tool, however, provides a standalone way to run this on pVACbind’s generated filtered/all_epitopes TSV files. For instance, this may be desired if pvacbind was originally run without this specified and one wished to perform this additional step after the fact for the filtered TSV—or perhaps instead the results of this were desired for the all_epitopes TSV which does not have this step performed. For a closer look at the generated reference_match file, see the pVACbind output file documentation.
NetChop Predict Cleavage Sites¶
usage: pvacbind net_chop [-h] [--method {cterm,20s}] [--threshold THRESHOLD]
input_file input_fasta output_file
Predict cleavage sites for neoepitopes.
positional arguments:
input_file Input filtered file with predicted epitopes.
input_fasta The required fasta file.
output_file Output tsv filename for putative neoepitopes.
optional arguments:
-h, --help show this help message and exit
--method {cterm,20s} NetChop prediction method to use ("cterm" for C term
3.0, "20s" for 20S 3.0). (default: cterm)
--threshold THRESHOLD
NetChop prediction threshold. (default: 0.5)
This tool uses NetChop to predict cleavage sites for neoepitopes from a pVACbind run’s filtered/all_epitopes TSV. In its output, it adds to the TSV 3 columns: Best Cleavage Position, Best Cleavage Score, and a Cleavage Sites list. Typically this step is done in the pVACbind run pipeline for the filtered output TSV when specified. This tool provides a way to manually run this on pVACbind’s generated filtered/all_epitopes TSV files so that you can add this information when not present if desired. You can view more about these columns for pVACbind in the output file documentation.
NetMHCStab Predict Stability¶
usage: pvacbind netmhc_stab [-h] [-m {lowest,median}] input_file output_file
Add stability predictions to predicted neoepitopes.
positional arguments:
input_file Input filtered file with predicted epitopes.
output_file Output TSV filename for putative neoepitopes.
optional arguments:
-h, --help show this help message and exit
-m {lowest,median}, --top-score-metric {lowest,median}
The ic50 scoring metric to use when sorting epitopes.
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)
This tool uses NetMHCstabpan to add stability predictions for neoepitopes from a pVACbind run’s filtered/all_epitopes TSV. In its output, it adds to the TSV 4 columns: Predicted Stability, Half Life, Stability Rank, and NetMHCStab Allele. Typically this step is done in the pVACbind run pipeline for the filtered output TSV when specified. This tool provides a way to manually run this on pVACbind’s generated filtered/all_epitopes TSV files so that you can add this information when not present if desired. You can view more about these columns for pVACbind in the output file documentation.