Name: immuno
Owner: Hammer Lab
Description: Use somatic mutations to choose a personalized cancer vaccine (tumor-specific immunogenic peptides)
Created: 2014-03-06 19:56:01.0
Updated: 2017-02-17 20:45:04.0
Pushed: 2016-09-23 20:53:08.0
Homepage: null
Size: 2583
Language: Python
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on mutation_report.py --string EDLTVKIGDFGLATEKSRWSGSHQFEQLS --hla "HLA-B*35:01"
on 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 outputYou must either have netMHCpan installed locally or pass the iedb-mhc flag to use a web-based MHC binding predictor.