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LiftOff

Definition
AI-generated

LiftOff is a tool that projects gene annotation from one genome assembly to another by aligning gene sequences and introns to the target assembly, preserving splice structure where possible.

Topics
Post-GWAS
URL
https://github.com/agshumate/Liftoff
Related
Genome Annotation LiftOn LiftOver

Why it matters in GWAS

Meta-analyses and multi-cohort pipelines must keep variant coordinates and gene boundaries on a consistent build; lifting variants without reconciling annotation can break exon overlap checks. LiftOff helps migrate curated gene models rather than re-annotating from scratch.

Example usage

"We lifted the prior GFF from CHM13 to hg38 with LiftOff for consistent gene windows with the GWAS panel."

Genome Annotation LiftOn LiftOver Variant Annotation
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Shumate A, Salzberg SL. (2021). Liftoff: accurate mapping of gene annotations. Bioinformatics.
  • Ji HJ, Pertea M, Salzberg SL. (2026). Annotating genomes at increased scale and resolution. Nat Rev Genet. https://doi.org/10.1038/s41576-026-00937-3
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