Predict cancer epitopes from cancer sequence data
Project description
Predict mutation-derived cancer T-cell epitopes from (1) somatic variants (2) tumor RNA expression data, and (3) patient HLA type.
Example
./topiary \
--vcf somatic.vcf \
--mhc-pan \
--mhc-alleles HLA-A*02:01,HLA-B*07:02 \
--ic50-cutoff 500 \
--percentile-cutoff 2.0 \
--mhc-epitope-lengths 8-11 \
--rna-gene-fpkm-file genes.fpkm_tracking \
--rna-min-gene-expression 4.0 \
--rna-transcript-fpkm-file isoforms.fpkm_tracking \
--rna-min-transcript-expression 1.5 \
--output-csv epitopes.csv \
--output-html epitopes.html
Commandline Arguments
Genomic Variants
You must specify at least one variant input file:
Output Format
--output-csv OUTPUT_CSV_FILENAME: Path to an output CSV file
--output-html OUTPUT_HTML_FILENAME: Path to an output HTML file
RNA Expression Filtering
Optional flags to use Cufflinks expression estimates for dropping epitopes arising from genes or transcripts that are not highly expressed.
--rna-gene-fpkm-file RNA_GENE_FPKM_FILE: Cufflinks FPKM tracking file containing gene expression estimates.
--rna-min-gene-expression RNA_MIN_GENE_EXPRESSION: Minimum FPKM for genes
--rna-remap-novel-genes-onto-ensembl: If a novel gene is fully contained within a known Ensembl gene, remap its FPKM expression value on the Ensembl gene ID.
--rna-transcript-fpkm-file RNA_TRANSCRIPT_FPKM_FILE: Cufflinks FPKM tracking file containing transcript expression estimates.
--rna-min-transcript-expression RNA_MIN_TRANSCRIPT_EXPRESSION: Minimum FPKM for transcripts
Choose an MHC Binding Predictor
You must choose an MHC binding predictor using one of the following flags:
--mhc-pan: Local NetMHCpan
--mhc-cons: Local NetMHCcons
--mhc-random: Random IC50 values
--mhc-smm: Local SMM
--mhc-smm-pmbec: Local SMM-PMBEC
--mhc-pan-iedb: NetMHCpan via the IEDB web API
--mhc-cons-iedb: NetMHCcons via the IEDB web API
--mhc-smm-iedb: SMM via the IEDB web API
--mhc-smm-pmbec-iedb: SMM-PMBEC via the IEDB web API
MHC Alleles
You must specify the alleles to perform binding prediction for using one of the following flags:
--mhc-alleles-file MHC_ALLELES_FILE: Text file containing one allele name per line
--mhc-alleles MHC_ALLELES: Comma separated list of allele names, e.g. “HLA-A02:01,HLA-B07:02”
Peptide Length
--mhc-epitope-lengths MHC_EPITOPE_LENGTHS: comma separated list of integers specifying which peptide lengths to use for MHC binding prediction
Binding Prediction Filtering
--keep-wildtype-epitopes: Topiary will normally discard predicted epitopes which don’t overlap a mutated region of a protein. Use this flag to keep all predicted epitopes you must this
--ic50-cutoff IC50_CUTOFF: Drop peptides with predicted IC50 nM greater than this value (typical value is 500.0)
--percentile-cutoff PERCENTILE_CUTOFF: Drop peptides with percentile rank of their predicted IC50 (among predictions for a particular allele) fall below this threshold (lower values are stricter filters, typical value is 2.0)
Misc
--padding-around-mutation PADDING_AROUND_MUTATION: Include more unmutated residues around the mutation (useful when combined with --keep-wildtype-epitopes)
--self-filter-directory SELF_FILTER_DIRECTORY: Directory of files named by MHC allele containing a self peptide ligandome (peptides which should be excluded from results)
--skip-variant-errors: If a particular mutation causes an exception to be raised during annotation, you can skip it using this flag.
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