25 May 2011:: SVA is published in Bioinformatics.

21 Mar 2011:: SVA V1.10 is released: [1]Supports GRCh build 37/hg19; [2] Supports user annotation track in GFF3 or BED formats.

9 Sep 2010:: The characterization of twenty sequenced human genomes. [Article]

12 Jul 2010:: LabCorp Launches Interleukin 28B Polymorphism (IL28B) Genotype Test to Support Individualized Treatment Decisions for Patients with Hepatitis C Viral Infection.

17 Jun 2010:: Causal variants for metachondromatosis are identified.
[Article] [SVA screenshot]
[GenomeWeb: The Daily Scan]

18 Mar 2010:: SVA 1.02[beta] is released.

11 Mar 2010:: SVA 1.01[beta] is released with a command line tool.

8 Mar 2010:: A lite evaluation edition is released for Windows. Play with it on your laptop!

23 Jan 2010:: SVA 1.00[beta] is released.


DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit ( Bentley et al. Nature 2008; 456:53-59 ). Compared with previous discovery strategies, a whole-genome sequencing study is no longer constrained by differing patterns of linkage disequilibrium ( Need and Goldstein, Trends in Genetics 2009;25(11):489-494 ), thus, in theory, is more possible to directly identify the genetic variants contributing to biological traits or medical outcomes.

The rapidly evolving high-throughput DNA sequencing technologies have now allowed the fast generation of large amount of sequence data for the purpose of performing such whole-genome sequencing studies, at a reasonable cost. S equence V ariant A nalyzer, or SVA , is a software tool that we have been developing to analyze the genetic variants identified from such studies.


SVA is designed for two specific aims:

(1) To annotate the biological functions of the identified genetic variants, visualize and organize them;

(2) To help find the genetic variants associated with or responsible for the biological traits or medical outcomes of interest.


SVA is:

a program designed to run on a LINUX platform, with a graphical user interface (GUI), meaning that the main functions of this program can be done with clicking buttons.

a program specifically designed for analyzing genetic variants that have already been called (identified) from a whole genome sequencing study. So do not try to find a function here to align short reads and call variants - SVA is not designed for those purposes - many other software tools, for example, BWA and SAMTOOLS , were developed for those purposes.

an extension to our previous program WGAViewer , a software tool aimed to facilitate the annotation and interpretation of Genome-wide Association studies (GWAS).

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© 2011 Dongliang Ge, PhD.