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Onkopus Functional Variant Interpretation

Use Case 1: Functional annotation- To annotate variant data, read in your data using a VCF reader or MAF reader node, followed by the corresponding '_to_Bframe' node in the source file's reference genome. - To combine multiple datasets, use the 'Combine datasets' node- Add the feature nodes you would like to annotate in the pipeline, e.g. 'Protein and transcript', 'Pathogenicity scores', 'Protein features'- Write the annotated variant data using a VCF, MAF or CSV writer node CSV_to_BFrameCSV-ReaderCombinedatasetsBFrameto_VCFVCF-WriterVariantsVCF-ReaderProtein_To_GenomicFunctionalregions(GENCODE)BFrameto_CSVPathogenicityscoresProtein featuresVCF_to_BFrame (GRCh38)CSV-WriterVariantsPython Script File Reader Python Script Python Script CSV Writer File Reader Python Script Python Script Python Script Python Script Python Script Python Script CSV Writer Use Case 1: Functional annotation- To annotate variant data, read in your data using a VCF reader or MAF reader node, followed by the corresponding '_to_Bframe' node in the source file's reference genome. - To combine multiple datasets, use the 'Combine datasets' node- Add the feature nodes you would like to annotate in the pipeline, e.g. 'Protein and transcript', 'Pathogenicity scores', 'Protein features'- Write the annotated variant data using a VCF, MAF or CSV writer node CSV_to_BFrameCSV-ReaderCombinedatasetsBFrameto_VCFVCF-WriterVariantsVCF-ReaderProtein_To_GenomicFunctionalregions(GENCODE)BFrameto_CSVPathogenicityscoresProtein featuresVCF_to_BFrame (GRCh38)CSV-WriterVariantsPython Script File Reader Python Script Python Script CSV Writer File Reader Python Script Python Script Python Script Python Script 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: 2025-02-08
Last update: 2025-03-31
Created with KNIME version: v5.3.2

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