Using this software0. For impatient users
1. Data inputs
2. Create a project
3. Annotate a project
Using user annotation track
4. Filter for quality scores
5. Main user interface
6. SVA genome browser
7. SVA tables
8. Selecting genes or regions
Bio-pathway or GO
Fisher's exact test
10. Exome or targeted capture sequencing
Using the command line tool
SVA version 1.01 and onwards comes with a command line tool, svacmd.sh . You can use this command tool to perform the main annotation and results exportation as a background run, without starting and holding the graphical user interface of SVA.
svacmd.sh itself is only a script. It does not perform any annotation job, but instead call the main SVA module to do the actual work.
The outputs of this command line tool include both the binary output directly readable by SVA graphical user interface, and a set of comma delimited text files exported for variant and subject details.
First of all, please correctly install this command line tool.
1. You should run the command line tool of SVA with this command:
The command line tool takes two parameters: 1. The amount of memory (RAM) you would like to allocate to SVA in megabytes (MB), and 2. The absolute, or canonical path of your SVA .gsap project file. You can create your .gsap project by copying and modifying the example project file.
It is very important to use the absolute, or canonical path of your SVA .gsap project file as the second parameter. The absolute path must start from the root (/), for example, '/user/MyName/Work/MyFile.gsap'. This is true even you are currently at your working directory and a relative path './[your file]' works for other programs. The SVA command line tool only recognizes the absolute, or canonical path of your SVA .gsap project file.
You can get the absolute, or canonical path of your current working directory by typing this command, if you are not familiar with a Linux platform:
So, in summary,
2. If you prefer a background run that won't be interrupted by your logout, you can try this:
(1) Save the above command line (command 1) into a script file, say MyScript.sh.
(2) Make this script executable:
(3) And then nohup it:
(4) Monitor the progress (if you want to):
The screen outputs will be directed to a file nohup.txt so you can inspect the progress and results. You can also monitor the process by this command:
This will give you a real-time update on the screen outputs.
(5) Terminate the progress (if you want to):
When you nohup it, you should have a process ID. Use this process ID to kill the background run if you want to. You can also try command top to find the process ID and kill it.
1. As you can see, SVA command line tool needs to start from its installation directory. - This merely was set for consistence with earlier behaviors of JAVA programs on a Mac.
© 2011 Dongliang Ge, PhD.