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LiftOver

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 or T2T-CHM13, be sure to insert a liftover node ("Liftover (GRCh37 to GRCh38)", or "Liftover (T2T)") node to your annotation pipeline before adding any annotation nodes. GRCh37 to GRCh38 / T2T-CHM13 GRCh38 to GRCh37 / T2T-CHM13 T2T to GRCh37 / GRCh38 LiftOver (GRCh38 to GRCh37) VCF _ to_ BFrame (GRCh37) Conda Environment VCF-Reader VCF-Reader VCF-Reader LiftOver (GRCh37 to T2T LiftOver (GRCh37 to GRCh38) LiftOver (T2T to GRCh37) LiftOver (T2T to GRCh37) LiftOver (GRCh38 to T2T) VCF _ to_ BFrame (GRCh38) VCF _ to_ BFrame (T2T-CHM13) VCF-Writer Variants BFrame to_VCF VCF-Writer Variants BFrame to_VCF BFrame to_VCF VCF-Writer Variants BFrame to_VCF VCF-Writer Variants BFrame to_VCF VCF-Writer Variants BFrame to_VCF VCF-Writer Variants Conda Environment Conda Environment Python Script Python Script Conda Environment Propagation File Reader File Reader File Reader Python Script Python Script Python Script Python Script Python Script Python Script Python Script CSV Writer Python Script CSV Writer Python Script Python Script CSV Writer Python Script CSV Writer Python Script CSV Writer Python Script CSV Writer Conda Environment Propagation Conda Environment Propagation 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 or T2T-CHM13, be sure to insert a liftover node ("Liftover (GRCh37 to GRCh38)", or "Liftover (T2T)") node to your annotation pipeline before adding any annotation nodes. GRCh37 to GRCh38 / T2T-CHM13 GRCh38 to GRCh37 / T2T-CHM13 T2T to GRCh37 / GRCh38 LiftOver (GRCh38 to GRCh37) VCF _ to_ BFrame (GRCh37) Conda Environment VCF-Reader VCF-Reader VCF-Reader LiftOver (GRCh37 to T2T LiftOver (GRCh37 to GRCh38) LiftOver (T2T to GRCh37) LiftOver (T2T to GRCh37) LiftOver (GRCh38 to T2T) VCF _ to_ BFrame (GRCh38) VCF _ to_ BFrame (T2T-CHM13) VCF-Writer Variants BFrame to_VCF VCF-Writer Variants BFrame to_VCF BFrame to_VCF VCF-Writer Variants BFrame to_VCF VCF-Writer Variants BFrame to_VCF VCF-Writer Variants BFrame to_VCF VCF-Writer Variants Conda Environment Conda Environment Python Script Python Script Conda Environment Propagation File Reader File Reader File Reader Python Script Python Script Python Script Python Script Python Script Python Script Python Script CSV Writer Python Script CSV Writer Python Script Python Script CSV Writer Python Script CSV Writer Python Script CSV Writer Python Script CSV Writer Conda Environment Propagation Conda Environment Propagation

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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: 2025-06-04
On NodePit since: 2025-06-26
Last update: 2025-07-25
Created with KNIME version: v5.4.3

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