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01 - Basic annotation workflow

Variant annotation: Workflow basics - 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. - Annotation nodes have a biomarker frame both as input and output, i.e. a JSON-based internal representation of the annotated variant data. Annotation modules can thus be freely sequentially aligned in an annotation workflow - Some modules rely on annotations of other modules (e.g. protein annotation). In that case, make sure to annotate with the required module first. Check out the required pre-annotations of a node by hovering over a node with the mouse.
Protein_annotation
Python Script
Set up python env
Python Script
VCF-Reader
File Reader
Functionalregions
Python Script
BFrameto_VCF
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: 2025-07-10
On NodePit since: 2025-10-27
Last update: 2025-10-30
Created with KNIME version: v5.8.0

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