topiary 0.0.3

Predict cancer epitopes from cancer sequence data

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:

• --vcf VCF_FILENAME: Load a VCF file

• --maf MAF_FILENAME: Load a TCGA MAF 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”

MHC Binding Options

• --mhc-epitope-lengths MHC_EPITOPE_LENGTHS: comma separated list of integers specifying which peptide lengths to perform MHC binding prediction for

Misc

• --padding-around-mutation PADDING_AROUND_MUTATION

• --self-filter-directory SELF_FILTER_DIRECTORY

• --skip-variant-errors