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03 - Functional variant annotation

Functional variant annotation - A workflow to annotate single nucleotide variants (SNVs) and small insertions and deletions (InDels) - 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. - 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
Protein_To_Genomic
Python Script
Set up python env
Python Script
Functionalregions(GENCODE)
Python Script
VCF-Reader
File Reader
BFrameto_VCF
Python Script
Protein features
Python Script
Pathogenicityscores
Python Script
VCF-WriterVariants
CSV Writer
VCF_to_BFrame (GRCh38)
Python Script

Nodes

Extensions

Links

Download

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

Download Workflow
Created by: nadine
Created at: 2025-06-04
On NodePit since: 2025-10-27
Last update: 2025-10-30
Created with KNIME version: v5.8.0

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