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

Get Started

wANNOVAR is updated to 2024 version. You can submit new jobs now.

By default, wANNOVAR performs "individual analysis" on the first sample in your VCF file to help find disease genes (you may need to split your multi-sample VCF file to individual files for annotation separately to find disease genes). If you only want to annotate all variant sites in a multi-sample VCF file, select "All Annotations" option below (for example, if your VCF contains variant calls for a pair of normal and tumor sample, or if your VCF contains variants for a parent-offspring trio). You will get a "unable to read uploaded ANNOVAR input file" error if you upload a VCF with a pair of normal/tumor sample because normal sample has no genotypes from typical somatic variant calling tools such as Mutect.

If you see an error message "cannot create submission directory for submission: no space left", it means our server's storage space is full. You can wait 1-2 days to submit again, or you can email Kai to resolve the issue quickly.

Basic Information

Sample Identifier

Input File

or Paste Variant Calls

Monitor Progress

I agree to the Terms of Use . Please note that commerical users would need to obtain a license.

Disease/Phenotype

Enter Disease or Phenotype Terms

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.

Parameter Settings

Result duration

Reference Genome

Input Fomat

Gene Definition

Individual analysis

Disease Model

Custom Filtering

Quality threshold

MAF

dbSNP Version

disease type

recessive dominant unknown

Variant filters

Not in control

user provided control variants

Control File

or Paste Variant Calls

Recent Updates

[7/12/2024] The wANNOVAR server is updated to 2024 version with dbNSFP v4.7a and gnomAD v4.1 (hg38) or gnomAD v2.1.1 (hg19).

[12/3/2023] The wANNOVAR server is migrated to a new host. I plan to add functionality to handle hs1 (T2T-CHM13) soon. I will also include the latest version of dbNSFP and gnomAD.

[5/9/2019] The wANNOVAR server is migrated to a new host. All submissions will be deleted within 1 day (new rule in June 2019) due to lack of storage space. Please download your results promptly.

[10/19/2017] The detailed amino acid changes for indels are now included in the output (through -polish argument in table_annovar). The server also handles duplicated entries (multiple identical variants) in the input file correctly.

[08/25/2017] The variants reduction method (for disease gene finding from personal genomes) has been updated to the latest version.

[07/31/2017] All databases are updated to 20170517 version.

[10/22/2015] Now the filter is working for hg38! However, the custom filter is 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!