wANNOVAR

ANNOVAR is a rapid, efficient tool to annotate functional consequences of genetic variation from high-throughput sequencing data. wANNOVAR provides easy and intuitive web-based access to the most popular functionalities of the ANNOVAR software

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Input File
Monitor Progress


Please use semicolon or enter as separators. Like "alzheimer;brain".
Try to use multiple terms instead of a super long term
OMIM IDs are also accepted, like 114480 for 'Breast cancer'
Better Combined with wANNOVAR's disease model.
Control File

[10/22/2015] Now the filter is working for hg38! However, the custom filter is still not supported

[07/16/2015] Now we added another select called 'Individual Analysis', which is designed for VCF files. If you want to include all the individuals in your VCF file, please choose 'All annotations'. If you want to conduct individual based analysis (the first one if multiple samples are present), please choose 'Individual analysis'.

[04/01/2015] The ANNOVAR software have been updated to the newest version! hg38 reference genome was added!
The Disease Model has been modified and now the 'rare recessive Mendelian disease' and 'rare dominant Mendelian disease' don't exclude SNPs in dbSNP database any more!

[11/18/2014] Due to the users' complaints about our no longer supports of the multiple samples in omne vcf file, I added the VCFold format back in the 'Input Format' option, which still supports multiple samples in one vcf file.

[11/17/2014] The refGene, knownGene, ensGene have been updated to the newest versions! GWAS catalog annotation was added! ClinVar annotation was updated! The 1000g2014oct and ljb26 annotation is updated.

[10/03/2014] Please email yanghui@usc.edu your ID if you didn't receive your email! I will send your result URL to you.

Would you like to try our new wANNOVAR-Phenolyzer pipeline by entering your disease or phenotype? Now the prioritized genes with scores and variants are in the output.

[07/31/2014] The whole wANNOVAR is remade! The Phenotype/Disease specific candidate gene prioritization is added. Now the user could enter any disease/phenotype term together with variant file!

[02/24/2014] Now the dbSNP137, dbSNP138(only for hg19), 1000 Genomes Project 2012Apr release, LJB2 databases are updated. The column order in the result file was adjusted to be shown more intuitively. And because of the spam attacks, the invalid input is not accepted anymore.

[11/06/2013] Many users have complained about constant "lack of space" error message in the server. We are looking into a solution, possibly moving wANNOVAR to another host that provides more storage space.

[02/24/2013]The annotation column is also updated from ESP5400 to ESP6500.

[11/26/2012] The NHLBI-ESP 5400 exomes is updated to the latest NHLBI-ESP 6500 exomes. A new custom filtering step is added to remove common variants from 46 whole genomes sequenced by Complete Genomics.

[05/14/2012] Advanced options are now available to users, including selection of dbSNP version, MAF threshold and customized variants reduction pipeline.

[03/08/2012] The wANNOVAR server is updated to use the latest version of the ANNOVAR software and database, including dbSNP 135 and 1000 Genomes Project 2012Feb release.