SequenceVariantAnalyzer

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Application data

Created by Dongliang Ge & David Goldstein
Biological application domain(s) Personalised medicine, Genomics, Sequence analysis, Genetic variation
Principal bioinformatics method(s) Annotation, Genome visualisation, SNP calling
Created at Duke University
Maintained? Yes
Input format(s) SAMtools, HMMCNV
Output format(s) sva
Software features Variant annotation and analysis
Programming language(s) Java
Operating system(s) Linux 64

Summary: DNA sequence information underpins genetic research, enabling discoversies of important biological or medical benefit. Compared with previous discovery strategies, a whole-genome sequencing study is no longer constrained by differing patterns of linkage disequilibrium, thus, in theory, is more possible to directly identify the gentic 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. SequenceVariantAnalyzer, or SVA, is a software tool that we have been developing to analyze the genetic variants identified from such studies. URL: http://www.svaproject.org/

Sva.jpg

SequenceVariantAnalyzer (SVA)

http://www.svaproject.org/

DNA sequence information underpins genetic research, enabling discoversies 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 gentic 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. SequenceVariantAnalyzer, 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 and group them, conveniently;

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

It 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.

It is 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.

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

It is being developed by Drs. Dongliang Ge and David Goldstein at Duke University Institute for Genome Sciences & Policy (IGSP), Center for Human Genome Variation. The SVA project is supported by Duke University Institute for Genome Sciences & Policy and partly by a research grant from The Bill & Melinda Gates Foundation awarded to David Goldstein. SVA is available to the research community free of charge.

For questions and comments, please contact Dr. Dongliang Ge at: [email protected] .

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