VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era.

Journal Article (Journal Article)

VarioWatch ( has been vastly improved since its former publication GenoWatch in the 2008 Web Server Issue. It is now at least 10 000-times faster in annotating a variant. Drastic speed increase, through complete re-design of its working mechanism, makes VarioWatch capable of annotating millions of human genomic variants generated from next generation sequencing in minutes, if not seconds. While using MegaQuery of VarioWatch to quickly annotate variants, users can apply various filters to retrieve a subgroup of variants according to the risk levels, interested regions, etc. that satisfy users' requirements. In addition to performance leap, many new features have also been added, such as annotation on novel variants, functional analyses on splice sites and in/dels, detailed variant information in tabulated form, plus a risk level decision tree regarding the analyzed variant. Up to 1000 target variants can be visualized with our carefully designed Genome View, Gene View, Transcript View and Variation View. Two commonly used reference versions, NCBI build 36.3 and NCBI build 37.2, are supported. VarioWatch is unique in its ability to annotate comprehensively and efficiently millions of variants online, immediately delivering the results in real time, plus visualizes up to 1000 annotated variants.

Full Text

Duke Authors

Cited Authors

  • Cheng, Y-C; Hsiao, F-C; Yeh, E-C; Lin, W-J; Tang, C-YL; Tseng, H-C; Wu, H-T; Liu, C-K; Chen, C-C; Chen, Y-T; Yao, A

Published Date

  • July 2012

Published In

Volume / Issue

  • 40 / Web Server issue

Start / End Page

  • W76 - W81

PubMed ID

  • 22618869

Pubmed Central ID

  • PMC3394242

Electronic International Standard Serial Number (EISSN)

  • 1362-4962

Digital Object Identifier (DOI)

  • 10.1093/nar/gks397


  • eng

Conference Location

  • England