Package: topiary
Predict mutation-derived cancer T-cell epitopes from (1) somatic
variants (2) tumor RNA expression data, and (3) patient HLA type.Example./topiary\--vcfsomatic.vcf\--mhc-predictornetmhcpan\--mhc-allelesHLA-A*02:01,HLA-B*07:02\--ic50-cutoff500\--percentile-cutoff2.0\--mhc-epitope-lengths8-11\--rna-gene-fpkm-tracking-filegenes.fpkm_tracking\--rna-min-gene-expression4.0\--rna-transcript-fpkm-tracking-fileisoforms.fpkm_tracking\--rna-min-transcript-expression1.5\--output-csvepitopes.csv\--output-htmlepitopes.htmlInstallationYou can install Topiary and all of the libraries it depends on by
running:pip install topiaryYou’ll need to download the reference genome sequences and annotations
for a recent Ensembl release (e.g. 81) by running:pyensembl install --release 81 --species humanIf you want to work with variants which were aligned against the older
reference GRCh37, you will need to also download its annotation data,
which is contained in Ensembl release 75:pyensembl install --release 75 --species humanCommandline ArgumentsGenomic VariantsSpecify some variants by giving at least one of the following options.
They can be used in combination and repeated.--vcfVCF_FILENAME: Load aVCFfile--mafMAF_FILENAME: Load a TCGAMAFfile--variantCHR POS REF ALT : Specify an individual variant (requires--ensembl-version)Output Format--output-csvOUTPUT_CSV_FILENAME: Path to an output CSV file--output-htmlOUTPUT_HTML_FILENAME: Path to an output HTML fileRNA Expression FilteringOptional flags to use Cufflinks expression estimates for dropping
epitopes arising from genes or transcripts that are not highly
expressed.--rna-gene-fpkm-tracking-fileRNA_GENE_FPKM_TRACKING_FILE:
Cufflinks FPKM tracking file containing gene expression estimates.--rna-min-gene-expressionRNA_MIN_GENE_EXPRESSION: Minimum FPKM
for genes--rna-transcript-fpkm-tracking-fileRNA_TRANSCRIPT_FPKM_TRACKING_FILE:
Cufflinks FPKM tracking file containing transcript expression
estimates.--rna-min-transcript-expressionRNA_MIN_TRANSCRIPT_EXPRESSION:
Minimum FPKM for transcripts--rna-transcript-fpkm-gtf-fileRNA_TRANSCRIPT_FPKM_GTF_FILE:
StringTie GTF file file containing transcript expression estimates.Choose an MHC Binding PredictorYoumustchoose an MHC binding predictor using one of the following
values for the--mhc-predictorflag:netmhc: LocalNetMHCpredictor (Topiary will attempt to automatically detect whether
NetMHC 3.x or 4.0 is available)netmhcpan: LocalNetMHCpanpredictornetmhciipan: LocalNetMHCIIpanpredictornetmhccons: LocalNetMHCconsrandom: Random IC50 valuessmm: LocalSMMpredictorsmm-pmbec: LocalSMM-PMBECpredictornetmhcpan-iedb: Use NetMHCpan via the IEDB web APInetmhccons-iedb: Use NetMHCcons via the IEDB web APIsmm-iedb: Use SMM via the IEDB web APIsmm-pmbec-iedb: Use SMM-PMBEC via the IEDB web APIMHC AllelesYou must specify the alleles to perform binding prediction for using one
of the following flags:--mhc-alleles-fileMHC_ALLELES_FILE: Text file containing one
allele name per line--mhc-allelesMHC_ALLELES: Comma separated list of allele names,
e.g. “HLA-A02:01,HLA-B07:02”Peptide Length--mhc-epitope-lengthsMHC_EPITOPE_LENGTHS: comma separated list
of integers specifying which peptide lengths to use for MHC binding
predictionBinding 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-cutoffIC50_CUTOFF: Drop peptides with predicted IC50 nM
greater than this value (typical value is 500.0)--percentile-cutoffPERCENTILE_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-mutationPADDING_AROUND_MUTATION: Include more
unmutated residues around the mutation (useful when not using--only-novel-epitopes)--self-filter-directorySELF_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.