topiary 3.0.6

Genomic Variants

Specify some variants by giving at least one of the following options. They can be used in combination and repeated.

• --vcf VCF_FILENAME: Load a VCF file

• --maf MAF_FILENAME: Load a TCGA MAF file

• --variant CHR POS REF ALT : Specify an individual variant (requires --ensembl-version)

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-tracking-file RNA_GENE_FPKM_TRACKING_FILE: Cufflinks FPKM tracking file containing gene expression estimates.

• --rna-min-gene-expression RNA_MIN_GENE_EXPRESSION: Minimum FPKM for genes

• --rna-transcript-fpkm-tracking-file RNA_TRANSCRIPT_FPKM_TRACKING_FILE: Cufflinks FPKM tracking file containing transcript expression estimates.

• --rna-min-transcript-expression RNA_MIN_TRANSCRIPT_EXPRESSION: Minimum FPKM for transcripts

• --rna-transcript-fpkm-gtf-file RNA_TRANSCRIPT_FPKM_GTF_FILE: StringTie GTF file file containing transcript expression estimates.

Choose an MHC Binding Predictor

You must choose an MHC binding predictor using one of the following values for the --mhc-predictor flag:

• netmhc: Local NetMHC predictor (Topiary will attempt to automatically detect whether NetMHC 3.x or 4.0 is available)

• netmhcpan: Local NetMHCpan predictor

• netmhciipan: Local NetMHCIIpan predictor

• netmhccons: Local NetMHCcons

• random: Random IC50 values

• smm: Local SMM predictor

• smm-pmbec: Local SMM-PMBEC predictor

• netmhcpan-iedb: Use NetMHCpan via the IEDB web API

• netmhccons-iedb: Use NetMHCcons via the IEDB web API

• smm-iedb: Use SMM via the IEDB web API

• smm-pmbec-iedb: Use 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

• --only-novel-epitopes: Topiary will normally keep all predicted epitopes, even those which occur in a given self-ligandome or don’t overlap a mutated region of a protein. Use this flag to drop any epitopes which don’t contain mutations or that occur elsewhere in the self-ligandome.

• --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 not using --only-novel-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.