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Onkopus Node Overview

Data Reader Choose a reader node for your data, depending on the file type (VCF, MAF, CSV, XLSX, TXT) . To read in a variant data file, combine a file reader with the corresponding "_to_BFrame" node. Variant data can either be - at genomic level (e.g. 'chr7:g.140753336A>T') - AVF: Native Onkopus data format. Use this format if you want to read in your data again later inother workflows. - VCF: Community standard for DNA polymorphism data. Stores annotations in the INFO column. - MAF: Read in variant data from cancer studies (e.g. TCGA) data - at protein level (CSV, XLSX, TXT) (e.g. 'BRAF:p.V600E'): - CSV-Reader (Protein) - Your files should contain 2 columns labeled with "Protein" (e.g. "BRAF") and "Amino acidexchange" (e.g. "V600E") Liftover- Transform genome positions in other reference genome (Liftover) or - add positions in other reference genomes as annotations (Liftover annotation)NOTE: Onkopus modules annotate by default in GRCh38. If your data is in GRCh37,be sure to insert a "Liftover (GRCh37 to GRCh38)" node to your annotation pipelinebefore adding any annotation nodes. File writers Select a writer node that writes the results of your variant interpretation to your file system. - Variants Write you annotated variants to your file system. - VCF writer - MAF writer - CSV writer - Treatments Write clinical evidence of potential treatments to file - CSV_writer (Treatments): Writes clinical evidence data of potential treatments and their associated biomarkers to a file Annotation Annotates variant data with a variety of features - Protein: Maps a genomic level to a protein. Required for several other annotation modules - SeqCAT: Data on genomics and transcripts - dbSNP: Population frequency - dbNSFP: Large database containing many features, including pathogenicity scores and population frequency - MissensePathogenicity: Pathogenicity scores for missense variants (including AlphaMissense, REVEL, MVP, PrimateAI, CADD) - Protein features Information on the protein of the mutated positions, including domain, RSA, CA and secondary protein structure - ClinicalEvidence: Retrieves clinical evidence data on molecular targets from different databases (CIViC, OncoKB, MetaKB) - ClinVar: Human pathogenicity estimation Onkopus: Node Overview Create custom variant interpretation pipelines by sequentially aligning variant annotation modules to a pipeline. Start with a reader node to read in your variant data, add one or multiple Onkopus modules, and write your results to files by adding a writing node. Conversion (Genomic - Protein) Convert variant data at transcript or protein level to genomic level. After converting your data to genomic level, you may add additional Onkopus annotation modules. Filtering Add AdaGenes variant filters by adding an annotation module followed by a corresponding filter module ClinVarLoFToolVUSPredictMVPMetaKBOncoKBCIViCCSV_to_BFrameCSV-ReaderLiftOver annotation (GRCh37 to GRCh38)Filter dbSNP populationallelefrequency >1%InterpreterLiftOver (GRCh38 to GRCh37)LiftOver annotation (GRCh38 to GRCh37)LiftOver annotation (T2T to GRCh38)LiftOver annotation (T2T to GRCh37)LiftOver annotation (GRCh38 to T2T)LiftOver annotation (GRCh37 to T2T)AVF-ReaderAVF_to_BFrameMAF-WriterVariantsBFrameto_MAFPopulationfrequency(dbSNP, ExAC, 1000Genomes)Pathogenicityscores (all)Protein featuresAggregatorFunctionalregions(GENCODE)Complete annotationProtein_To_GenomicREVELAlphaMissenseProtein sequenceTranscript_To_GenomicBFrameto_CSVExportVariants (CSV)Filter ClinVar'Benign'Filter AlphaMissensescore < 0.8Filter variants in non-coding regionsVCF_to_BFrame (GRCh37)VCF-ReaderProtein_annotation (SeqCAT)VCF-ReaderVCF-ReaderLiftOver (GRCh37 to T2TLiftOver (GRCh37 to GRCh38)LiftOver (T2T to GRCh37)LiftOver (T2T to GRCh37)LiftOver (GRCh37 to GRCh38)TSV_to_BFrameTSV-ReaderXLSX_to_BFrameXLSX-ReaderTXT-ReaderTXT_to_BFrameMAF_to_BFrameMAF-ReaderClinical evidenceVCF_to_BFrame (GRCh38)VCF_to_BFrame (T2T-CHM13)Treatments_ExportExportTreatments (CSV)VCF-WriterVariantsBFrameto_VCFPython Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script File Reader Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script File Reader Python Script CSV Writer Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script CSV Writer Python Script Python Script Python Script Python Script File Reader Python Script File Reader File Reader Python Script Python Script Python Script Python Script Python Script Python Script File Reader Python Script File Reader File Reader Python Script Python Script File Reader Python Script Python Script Python Script Python Script CSV Writer CSV Writer Python Script Data Reader Choose a reader node for your data, depending on the file type (VCF, MAF, CSV, XLSX, TXT) . To read in a variant data file, combine a file reader with the corresponding "_to_BFrame" node. Variant data can either be - at genomic level (e.g. 'chr7:g.140753336A>T') - AVF: Native Onkopus data format. Use this format if you want to read in your data again later inother workflows. - VCF: Community standard for DNA polymorphism data. Stores annotations in the INFO column. - MAF: Read in variant data from cancer studies (e.g. TCGA) data - at protein level (CSV, XLSX, TXT) (e.g. 'BRAF:p.V600E'): - CSV-Reader (Protein) - Your files should contain 2 columns labeled with "Protein" (e.g. "BRAF") and "Amino acidexchange" (e.g. "V600E") Liftover- Transform genome positions in other reference genome (Liftover) or - add positions in other reference genomes as annotations (Liftover annotation)NOTE: Onkopus modules annotate by default in GRCh38. If your data is in GRCh37,be sure to insert a "Liftover (GRCh37 to GRCh38)" node to your annotation pipelinebefore adding any annotation nodes. File writers Select a writer node that writes the results of your variant interpretation to your file system. - Variants Write you annotated variants to your file system. - VCF writer - MAF writer - CSV writer - Treatments Write clinical evidence of potential treatments to file - CSV_writer (Treatments): Writes clinical evidence data of potential treatments and their associated biomarkers to a file Annotation Annotates variant data with a variety of features - Protein: Maps a genomic level to a protein. Required for several other annotation modules - SeqCAT: Data on genomics and transcripts - dbSNP: Population frequency - dbNSFP: Large database containing many features, including pathogenicity scores and population frequency - MissensePathogenicity: Pathogenicity scores for missense variants (including AlphaMissense, REVEL, MVP, PrimateAI, CADD) - Protein features Information on the protein of the mutated positions, including domain, RSA, CA and secondary protein structure - ClinicalEvidence: Retrieves clinical evidence data on molecular targets from different databases (CIViC, OncoKB, MetaKB) - ClinVar: Human pathogenicity estimation Onkopus: Node Overview Create custom variant interpretation pipelines by sequentially aligning variant annotation modules to a pipeline. Start with a reader node to read in your variant data, add one or multiple Onkopus modules, and write your results to files by adding a writing node. Conversion (Genomic - Protein) Convert variant data at transcript or protein level to genomic level. After converting your data to genomic level, you may add additional Onkopus annotation modules. Filtering Add AdaGenes variant filters by adding an annotation module followed by a corresponding filter module ClinVarLoFToolVUSPredictMVPMetaKBOncoKBCIViCCSV_to_BFrameCSV-ReaderLiftOver annotation (GRCh37 to GRCh38)Filter dbSNP populationallelefrequency >1%InterpreterLiftOver (GRCh38 to GRCh37)LiftOver annotation (GRCh38 to GRCh37)LiftOver annotation (T2T to GRCh38)LiftOver annotation (T2T to GRCh37)LiftOver annotation (GRCh38 to T2T)LiftOver annotation (GRCh37 to T2T)AVF-ReaderAVF_to_BFrameMAF-WriterVariantsBFrameto_MAFPopulationfrequency(dbSNP, ExAC, 1000Genomes)Pathogenicityscores (all)Protein featuresAggregatorFunctionalregions(GENCODE)Complete annotationProtein_To_GenomicREVELAlphaMissenseProtein sequenceTranscript_To_GenomicBFrameto_CSVExportVariants (CSV)Filter ClinVar'Benign'Filter AlphaMissensescore < 0.8Filter variants in non-coding regionsVCF_to_BFrame (GRCh37)VCF-ReaderProtein_annotation (SeqCAT)VCF-ReaderVCF-ReaderLiftOver (GRCh37 to T2TLiftOver (GRCh37 to GRCh38)LiftOver (T2T to GRCh37)LiftOver (T2T to GRCh37)LiftOver (GRCh37 to GRCh38)TSV_to_BFrameTSV-ReaderXLSX_to_BFrameXLSX-ReaderTXT-ReaderTXT_to_BFrameMAF_to_BFrameMAF-ReaderClinical evidenceVCF_to_BFrame (GRCh38)VCF_to_BFrame (T2T-CHM13)Treatments_ExportExportTreatments (CSV)VCF-WriterVariantsBFrameto_VCFPython Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script File Reader Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script File Reader Python Script CSV Writer Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script Python Script CSV Writer Python Script Python Script Python Script Python Script File Reader Python Script File Reader File Reader Python Script Python Script Python Script Python Script Python Script Python Script File Reader Python Script File Reader File Reader Python Script Python Script File Reader Python Script Python Script Python Script Python Script CSV Writer CSV Writer Python Script

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Created by: nadine
Created at: 2024-01-25
On NodePit since: 2025-01-23
Last update: 2025-03-31
Created with KNIME version: v5.3.2

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