SVA: Sequence Variant Analyzer







SequenceVariantAnalyzer, or SVA, is a computer software project designed to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies.

The ultimate goal of SVA is to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits.

SVA is free of charge to the research community in both academia and industry.

SVA software has contributed to a great number of scientific and industrial successes.

 

Download and Install

SVA software is free of charge to both academic and industrial researchers.

There are several steps to successfully download and install the SVA software package (human reference genome build 37, or hg19).

Step 1. Download the following three package files. Each file is around 250MB in size.

http://www.omicsexpress.com/software/sva/release/SequenceVariantAnalyzer_B37.7z.001

http://www.omicsexpress.com/software/sva/release/SequenceVariantAnalyzer_B37.7z.002

http://www.omicsexpress.com/software/sva/release/SequenceVariantAnalyzer_B37.7z.003

Step 2. Using 7zip (freely available at: http://www.7-zip.org/) to extract the downloaded package files from step 1, and put the extracted package to your hard drive [YOUR SVA DIR].

Step 3. Follow the following web links to visit Ensembl website, and download the listed data files. Note: if you are not using any FTP tool, then right click on the link and select "Save target as...".

ftp://ftp.ensembl.org/pub/release-61/mysql/homo_sapiens_variation_61_37f/allele.txt.gz

ftp://ftp.ensembl.org/pub/release-61/mysql/homo_sapiens_variation_61_37f/variation_feature.txt.gz

ftp://ftp.ensembl.org/pub/release-61/mysql/homo_sapiens_variation_61_37f/variation.txt.gz

ftp://ftp.ensembl.org/pub/release-61/mysql/homo_sapiens_core_61_37f/xref.txt.gz

ftp://ftp.ensembl.org/pub/release-61/mysql/homo_sapiens_core_61_37f/object_xref.txt.gz

Step 4. Using 7zip (freely available at: http://www.7-zip.org/) to extract the downloaded package files from step 3. Put the extracted .txt files to this directory:

[YOUR SVA DIR]/datasource/ensembl/61_37f/

You are done installation. To check if you have installed the package successfully, try to launch the program and load the example data set.

 

For more information, visit http://www.svaproject.org