Installation

Using this software

0. For impatient users
1. Data inputs
- Coordinate system
2. Create a project
3. Annotate a project
- Functional categories
- Using user annotation track
4. Filter for quality scores
5. Main user interface
6. SVA genome browser
- Sections overview
- Identified variants
- Public data
7. SVA tables
- SNV
- INDEL
- SV
8. Selecting genes or regions
- Gene symbol
- Bio-type
- Bio-pathway or GO
- OMIM disorder
- Genomic region
9. Analysis
- Gene prioritization
- Variant prioritization
- Fisher's exact test
10. Exome or targeted capture sequencing
A command line tool
FAQ
Requests and discussions

System requirment

 

SVA is a JAVA program, designed to run on a 64-bit LINUX platform with a 64-bit JAVA environment installed. SVA was designed to be a LINUX desktop software tool.

 

1. Hardware

 

Standard Full Edition

The minimum hardware requirement for SVA standard edition is a 64-bit LINUX workstation equipped with at least 32GB of RAM and 120GB of free hard disk. This workstation also needs to support a Graphical User Interface (GUI) environment, for example, using the X Window System.

However, we would like to recommend a 64-bit LINUX workstation equipped with 48GB of RAM or more, and 1TB of free hard disk or more.

The developers are using the machine specified below to run SVA and found it productive. Please note we do not intend to recommend the specific model or manufacturer, but rather list the specifications here for your reference.

  • DELL PowerEdge 2900 III: Quad Core Intel® Xeon® X5460, 2x6MB Cache, 3.16GHz, 1333MHz FSB
    Additional Processor: Quad Core Intel® Xeon® X5460, 2x6MB Cache, 3.16GHz, 1333MHz FSB
    Memory: 48GB 667MHz Dual Ranked DIMMs
    Operating System: Cent OS 5
    Primary Hard Drive: 500GB 7.2K RPM Universal SATA 3Gbps 3.5-in HotPlug Hard Drive
    2nd Hard Drive: 500GB 7.2K RPM Universal SATA 3Gbps 3.5-in HotPlug Hard Drive
    3rd Hard Drive: 500GB 7.2K RPM Universal SATA 3Gbps 3.5-in HotPlug Hard Drive
    Monitor: 21 inch monitor

Lite Evaluation Edition

Please note this lite evaluation edition does not provide the full annotation functions, but can be only used to load the example dataset for testing purposes.

  1. You need about 3GB of RAM to load the example project with its genome browser data, and enabling 1000 Human Genome data option.
  2. You need about 0.5GB of RAM to load the example project with its genome browser data, and disabling 1000 Human Genome data option.
  3. You need about 0.3GB RAM to load the example project without its genome browser data, and disabling 1000 Human Genome data option. In this case you will be able to list the annotated variants, but cannot search genes in the SVA Genome Browser panel, or perform following analysis or listing functions.
  4. You cannot perform any new annotations using the lite evaluation edition.

 

2. Software

 

A 64-bit Sun JAVA environment with version no earlier than 1.6.0_17 is required to run SVA. For details of JAVA releases, visit Sun JAVA website.

Important note:

(1) JAVA has to be correctly installed, which means that JAVA is correctly added into your system path. Otherwise, SVA will throw a "Configuration error" exception and will not start.

In other words, if you do not add JAVA into your system path, you cannot start SVA by executing this command by directly calling JAVA path:

[YOUR JAVA PATH]/java -jar SequenceVariantAnalyzer.jar

(2) SVA is compiled using the Sun JAVA (http://www.java.com/). It is known that it does not run properly in an OpenJDK environment.

 

If you desire to access SVA through a Windows PC to a LINUX workstation or server, a PC X server then is necessary. Multiple such products are available, for example, X-Win32 .

For Mac users, X server may be available from the operating system. You may try "ssh -x [your LINUX server]" to establish such connection. Or you may need additional software tool, like X11.

 
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