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Filtering Add AdaGenes variant filters by adding an annotation module followed by a corresponding filter module 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. 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 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 in other 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 acid exchange" (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 pipeline before adding any annotation nodes. Python Environment Use this node to set up a Conda environment to make sure the Python nodes work correctly. ClinVar LoFTool VUSPredict MVP MetaKB OncoKB CIViC CSV _ to_ BFrame CSV -Reader LiftOver annotation (GRCh37 to GRCh38) Filter dbSNP population allele frequency >1% Interpreter LiftOver (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-Reader AVF_ to_ BFrame Population frequency (dbSNP, ExAC, 1000Genomes) Pathogenicity scores (all) Protein features Aggregator Functional regions (GENCODE) Complete annotation Protein_To _Genomic REVEL AlphaMissense Protein sequence Transcript_To _Genomic BFrame to_CSV Export Variants (CSV) Filter ClinVar 'Benign' Filter AlphaMissense score < 0.8 Filter variants in non-coding regions VCF _ to_ BFrame (GRCh37) Variant interpretation Conda Environment VCF-Reader Protein_annotation (SeqCAT) VCF-Reader VCF-Reader LiftOver (GRCh37 to T2T LiftOver (GRCh37 to GRCh38) LiftOver (T2T to GRCh37) LiftOver (T2T to GRCh37) LiftOver (GRCh38 to T2T) TSV _ to_ BFrame TSV -Reader XLSX_ to_ BFrame XLSX -Reader TXT -Reader TXT_ to_ BFrame MAF_ to_ BFrame MAF-Reader Clinical evidence VCF _ to_ BFrame (GRCh38) VCF _ to_ BFrame (T2T-CHM13) Treatments_ Export Export Treatments (CSV) VCF-Writer Variants BFrame to_VCF Drug classification BFrame to_MAF MAF-Writer Variants Molecular features Python 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 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 Conda Environment Propagation 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 Python Script Python Script CSV Writer Python Script Filtering Add AdaGenes variant filters by adding an annotation module followed by a corresponding filter module 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. 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 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 in other 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 acid exchange" (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 pipeline before adding any annotation nodes. Python Environment Use this node to set up a Conda environment to make sure the Python nodes work correctly. ClinVar LoFTool VUSPredict MVP MetaKB OncoKB CIViC CSV _ to_ BFrame CSV -Reader LiftOver annotation (GRCh37 to GRCh38) Filter dbSNP population allele frequency >1% Interpreter LiftOver (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-Reader AVF_ to_ BFrame Population frequency (dbSNP, ExAC, 1000Genomes) Pathogenicity scores (all) Protein features Aggregator Functional regions (GENCODE) Complete annotation Protein_To _Genomic REVEL AlphaMissense Protein sequence Transcript_To _Genomic BFrame to_CSV Export Variants (CSV) Filter ClinVar 'Benign' Filter AlphaMissense score < 0.8 Filter variants in non-coding regions VCF _ to_ BFrame (GRCh37) Variant interpretation Conda Environment VCF-Reader Protein_annotation (SeqCAT) VCF-Reader VCF-Reader LiftOver (GRCh37 to T2T LiftOver (GRCh37 to GRCh38) LiftOver (T2T to GRCh37) LiftOver (T2T to GRCh37) LiftOver (GRCh38 to T2T) TSV _ to_ BFrame TSV -Reader XLSX_ to_ BFrame XLSX -Reader TXT -Reader TXT_ to_ BFrame MAF_ to_ BFrame MAF-Reader Clinical evidence VCF _ to_ BFrame (GRCh38) VCF _ to_ BFrame (T2T-CHM13) Treatments_ Export Export Treatments (CSV) VCF-Writer Variants BFrame to_VCF Drug classification BFrame to_MAF MAF-Writer Variants Molecular features Python 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 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 Conda Environment Propagation 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 Python Script Python Script CSV Writer Python Script

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Created by: nadine
Created at: 2025-06-04
On NodePit since: 2025-10-18
Last update: 2025-10-18
Created with KNIME version: v5.4.3

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