SequenceVariantAnalyzer
SequenceVariantAnalyzer (SVA) is a computer program for annotating and analyzing genetic variants called (identified) from a whole genome or exome sequencing study (Shotgun sequencing).
Introduction
[edit | edit source]Background
[edit | edit source]DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit.[1] Compared with previous discovery strategies, a whole-genome sequencing study is no longer constrained by differing patterns of linkage disequilibrium,[2] 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 rapid generation of large amounts of sequence data for the purpose of performing such whole-genome sequencing studies, at a reasonable cost. SequenceVariantAnalyzer, or SVA, is software that analyzes genetic variants identified in such studies.
Functions
[edit | edit source]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.
Language
[edit | edit source]SVA is developed on the Java platform.
Authors
[edit | edit source]SVA is developed and maintained by Dr. Dongliang Ge and Dr. David B. Goldstein at Duke University, Center for Human Genome Variation.