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ANNOVAR

Definition
AI-generated

ANNOVAR is a software toolkit for annotating genetic variants against gene models, population frequency resources, predicted functional effects, and other external databases.

Topics
Post-GWAS
URL
https://annovar.openbioinformatics.org/
Related
Ensembl GENCODE Genome Annotation

Why it matters in GWAS

After association or fine-mapping, researchers often use ANNOVAR to translate lead variants into transcript, gene, and frequency annotations. Results depend on the selected genome build, transcript set, and database versions, so those choices need to be reported for reproducibility.

Example usage

"We annotated lead SNPs with ANNOVAR against RefSeq transcripts and gnomAD frequencies on GRCh38 before pathway review."

Ensembl GENCODE Genome Annotation LiftOver RefSeq Variant Annotation Variant Effect Predictor (VEP)
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

  • Wang K, Li M, Hakonarson H. (2010). ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. https://doi.org/10.1093/nar/gkq603
  • GWASTutorial: Annotation by ANNOVAR & VEP.
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