RETIRED: See vaxrank and epidisco instead

Immunotherapy Pipeline

python mutation_report.py --string EDLTVKIGDFGLATEKSRWSGSHQFEQLS --hla "HLA-B*35:01"

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.

--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

You must either have netMHCpan installed locally or pass the iedb-mhc flag to use a web-based MHC binding predictor.