ANNOVAR

Overview

ANNOVAR (ANNOtate VARiation) is a bioinformatics tool for functionally annotating genetic variants identified by next-generation sequencing. It annotates SNVs and indels against multiple databases including gene function, conservation scores, disease associations, and population allele frequencies.

Used by

  • Applied in ICGC PedBrain pilocytic astrocytoma whole-genome sequencing study (96 cases) for functional annotation of somatic variants, used alongside oncotator; PCR + sanger-sequencing achieved >98% SNV verification PMID:23817572
  • Used for variant functional annotation in the grade II glioma exome sequencing study (n=23 paired initial/recurrent tumors) to annotate somatic mutations with gene, consequence, and population frequency information PMID:24336570
  • Used for variant functional annotation in the rhabdomyosarcoma genomic landscape study (147 tumor/normal pairs, WGS + WES + RNA-seq); run alongside Oncotator to annotate somatic mutations with gene consequence and population frequency PMID:24436047
  • Used for variant annotation in whole-genome and whole-exome sequencing of 28 uveal melanoma samples; identified PLCB4 p.D630Y as a recurrent gain-of-function hotspot mutually exclusive with GNAQ/GNA11 PMID:26683228.
  • ANNOVAR used for functional annotation of somatic variants called by the HGSC Mercury pipeline in 160 periampullary tumors, alongside COSMIC and dbSNP databases PMID:26804919
  • Used for variant annotation in MET500 whole-exome sequencing pipeline (500 metastatic solid tumors, GRCh37/hg19) alongside VarScan2 (SNVs) and Pindel (indels) PMID:28783718
  • Applied for variant annotation in the DLBCL 1001-tumor whole-exome sequencing analysis pipeline PMID:28985567
  • ANNOVAR used for functional annotation of somatic variants called in 15 Korean vulvar SCC tumor/normal WES pairs; PolyPhen-2 applied for missense impact prediction PMID:29422544

Notes

  • Corpus-grown slug; not found in cBioPortal canonical gene panel ontology.
  • Typically used downstream of alignment and variant calling (e.g., MuTect, Pindel), before biological interpretation.

Sources

This page was processed by crosslinker on 2026-05-14. - PMID:24336570

This page was processed by crosslinker on 2026-05-14. - PMID:24436047

This page was processed by crosslinker on 2026-05-14. - PMID:26683228

This page was processed by crosslinker on 2026-05-14. - PMID:26804919

This page was processed by wiki-cli on 2026-05-14. - PMID:28783718

This page was processed by entity-page-writer on 2026-05-15. - PMID:28985567

This page was processed by entity-page-writer on 2026-05-15. - PMID:29422544

This page was processed by wiki-cli on 2026-05-15.