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. 2019 Jul;7(7):e00641.
doi: 10.1002/mgg3.641. Epub 2019 May 24.

VCF-Server: A web-based visualization tool for high-throughput variant data mining and management

Jianping Jiang  1 , Jianlei Gu  1   2 , Tingting Zhao  1 , Hui Lu  1   2
Affiliations

VCF-Server: A web-based visualization tool for high-throughput variant data mining and management

Jianping Jiang et al. Mol Genet Genomic Med. 2019 Jul.

Abstract

Background: Next-generation sequencing (NGS) has been widely used in both clinics and research. It has become the most powerful tool for diagnosing genetic disorders and investigating disease etiology through the discovery of genetic variants. Variants identified by NGS are stored in variant call format (VCF) files. However, querying and filtering VCF files are extremely difficult for researchers without programming skills. Furthermore, as the mutation data are increasing exponentially, there is an urgent need to develop tools to manage these variant data in a centralized way.

Methods: The VCF-Server was developed as a web-based visualization tool to support the interactive analysis of genetic variant data. It allows researchers and medical geneticists to manage, annotate, filter, query, and export variants in a fast and effective way.

Results: In this study, we developed the VCF-Server, a powerful and easily accessible tool for researchers and medical geneticists to perform variant analysis. Users can query VCFs, annotate, and filter variants without knowing programming code. Once the VCF file is uploaded, VCF-Server allows users to annotate the VCF with commonly used databases or user-defined variant annotations (including variant blacklist and whitelist). Variant information in the VCF is shown visually via the interactive graphical interface. Users can filter the variants with flexible filtering rules, and the prioritized variants can be exported locally for further analysis. As VCF-Server adopts a web file system, files in the VCF-Server can be stored and managed in a centralized way. Moreover, VCF-Server allows direct web-based analysis (accessible through either desktop computers or mobile devices) as well as local deployment.

Conclusions: With an easy-to-use graphical interface, VCF-Server allows researchers with little bioinformatics background to explore and mine mutation data, which may broaden the application of NGS technology in clinics and research. The tool is freely available for use at https://www.diseasegps.org/VCF-Server?lan = eng.

Keywords: NGS; VCF visualization; software; variant filtering; variant management.

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Conflict of interest statement

The authors declare that they have no competing interests. The VCF‐Server is freely available, but the copyrights of all the annotation databases on VCF‐Server belong to the original copyright owners or organizations. If used for commercial purpose, the user must acquire the license(s) of annotation database(s) for commercial entities.

Figures

Figure 1
Figure 1
Hierarchical system design of VCF‐Server. VCF‐Server is a web application based on the Browser/Server architecture
Figure 2
Figure 2
VCF‐Server workflow. A public server has been provided for easy access, and local deployment is also possible. The user uploads one or more VCF files with or without whitelists/blacklists or private annotation databases. The back end stores data separately for each individual user and invokes different modules on demand. ⅰ, ⅱ, ⅲ and ⅳ are different application scenarios on the VCF‐Server
Figure 3
Figure 3
Screenshots of different functional modules on VCF‐Server. (a) VCF file management online. (b) Annotating VCF with commonly used annotation databases. (c) Variant filtering and visualization. (d) VCF index management
See this image and copyright information in PMC

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References

    1. Adzhubei, I. A. , Schmidt, S. , Peshkin, L. , Ramensky, V. E. , Gerasimova, A. , Bork, P. , … Sunyaev, S. R. (2010). A method and server for predicting damaging missense mutations. Nature Methods, 7(4), 248–249. 10.1038/nmeth0410-248 - DOI - PMC - PubMed
    1. Genomes Project, C. , Auton, A. , Brooks, L. D. , Durbin, R. M. , Garrison, E. P. , Kang, H. M. , … Abecasis, G. R. (2015). A global reference for human genetic variation. Nature, 526(7571), 68–74. 10.1038/nature15393 - DOI - PMC - PubMed
    1. Cancer Genome Atlas Research, N . (2008). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455(7216), 1061–1068. 10.1038/nature07385 - DOI - PMC - PubMed
    1. Carson, M. B. , Liu, C. , Lu, Y. , Jia, C. , & Lu, H. (2017). A disease similarity matrix based on the uniqueness of shared genes. BMC Medical Genomics, 10(Suppl 1), 26 10.1186/s12920-017-0265-2 - DOI - PMC - PubMed
    1. Cingolani, P. , Patel, V. M. , Coon, M. , Nguyen, T. , Land, S. J. , Ruden, D. M. , & Lu, X. (2012). Using drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift. Front Genet, 3, 35 10.3389/fgene.2012.00035 - DOI - PMC - PubMed

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