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Onkopus Variant Interpretation Workflows - Basics

Onkopus workflows: Basics - Create a variant interpretation workflow by adding a reader node and the corresponding '_to_Bframe' node in the source file's reference genome. - Onkopus works internally in GRCh38. If your source file's reference genome is not GRCh38, please add a LiftOver node to GRCh38 after reading in your file - Then add one or multiple annotation modules, e.g. population frequency, ClinVar annotation, pathogenicity scores, or molecular features. - To write your annotated variant data in a file, add a 'BFrame_to_VCF' node, followed by an 'Export variants (VCF)' node. Define your output file within the last node. You can also export your data in MAF, CSV, XLSX or TXT format. Onkopus Variant Interpretation Create your own customized variant annotation and interpretation workflows using the Onkopus framework. NOTE: Onkopus consults per default the public Onkopus web services available at mtb.bioinf.med.uni-goettingen.de. To annotate your data locally, install and run the Onkopus modules locally and add the following source code within each node: ONKOPUS_MODULE_PROTOCOL = 'http' ONKOPUS_MODULE_SERVER = 'localhost' ONKOPUS_PORTS_ACTIVE = 1 BFrameto_VCFVCF-WriterVariantsPopulationfrequencyPathogenicityscoresProteinVCF_to_BFrame (GRCh37)VCF-ReaderLiftOver (GRCh37 to GRCh38)BFrameto_CSVExportVariants (CSV)Python Script CSV Writer Python Script Python Script Python Script Python Script File Reader Python Script Python Script CSV Writer Onkopus workflows: Basics - Create a variant interpretation workflow by adding a reader node and the corresponding '_to_Bframe' node in the source file's reference genome. - Onkopus works internally in GRCh38. If your source file's reference genome is not GRCh38, please add a LiftOver node to GRCh38 after reading in your file - Then add one or multiple annotation modules, e.g. population frequency, ClinVar annotation, pathogenicity scores, or molecular features. - To write your annotated variant data in a file, add a 'BFrame_to_VCF' node, followed by an 'Export variants (VCF)' node. Define your output file within the last node. You can also export your data in MAF, CSV, XLSX or TXT format. Onkopus Variant Interpretation Create your own customized variant annotation and interpretation workflows using the Onkopus framework. NOTE: Onkopus consults per default the public Onkopus web services available at mtb.bioinf.med.uni-goettingen.de. To annotate your data locally, install and run the Onkopus modules locally and add the following source code within each node: ONKOPUS_MODULE_PROTOCOL = 'http' ONKOPUS_MODULE_SERVER = 'localhost' ONKOPUS_PORTS_ACTIVE = 1 BFrameto_VCFVCF-WriterVariantsPopulationfrequencyPathogenicityscoresProteinVCF_to_BFrame (GRCh37)VCF-ReaderLiftOver (GRCh37 to GRCh38)BFrameto_CSVExportVariants (CSV)Python Script CSV Writer Python Script Python Script Python Script Python Script File Reader Python Script Python Script CSV Writer

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: nadine
Created at: 2024-07-22
On NodePit since: 2025-01-25
Last update: 2025-04-29
Created with KNIME version: v5.3.2

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