RETIRED: See vaxrank and epidisco instead
Immunotherapy Pipeline
Status
Usage
From peptide string
python mutation_report.py --string EDLTVKIGDFGLATEKSRWSGSHQFEQLS --hla "HLA-B*35:01"From input file
python mutation_report.py --input-file <.vcf, .maf, .tab, .fasta> --hla-file <allele-file>
If VCF file is input, it will be annotated w/ gene information and Ensembl transcripts, otherwise input an annotated SnpEFF VCF file.
If you don't either an hla or hla-file then the default "HLA:A*02:01" will be used.
Options:
--input-file: Input file containing somatic variants (one of MAF, VCF, or SnpEff annotated VCF)--string: String of amino acids, with optional annotation of a mutated region between underscores (i.e. QYS_LL_Q)--hla: Comma separated list of HLA alleles.--hla-file: Text file containing one HLA allele per line.--peptide-length: Length of vaccine peptide (window around mutation, default 31)--min-peptide-padding: Minimum number of wildtype residues before or after a mutation--print-epitopes: Print dataframe with epitope scores--print-peptides: Print dataframe with vaccine peptide scores--output-epitopes-file: CSV output file for dataframe containing scored epitopes--output-report-file: Path to HTML report containing scored vaccine peptides and epitopes--random-mhc: Random values instead for MHC binding prediction--iedb-mhc: Use IEDB's web API for MHC binding--skip-mhc: Don't predict MHC binding--quiet: Suppress verbose output
Requirements
You must either have netMHCpan installed locally or pass the iedb-mhc flag to use a web-based MHC binding predictor.