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Sequence Variant Analyzer on Biowulf

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.

Program Location

/usr/local/sva

Memory requirement

SVA example project below need 3GBof RAM to load with it's genome browser data. So user can request g4 or g8 nodes for this. However, if user wants to perform new annotations with 1000 Human Genome data, request a g72 node since 48 GB of RAM or more is required.

Sample Sessions On Biowulf

SVA job can be run interactively on a node.

1. Allocate an interactive node

biowulf > qsub -I -V -l nodes=1:g4

2. Once your job started and a node is allocated to you, start a sva session:

p482> /usr/local/sva/SequenceVariantAnalyzer.sh&

A SequenceVariantAnalyzer window will pop up.

3. File-> Open SequenceVariantAnalyzer Project

This window shows. Select 'ExampleX.gsap' then click 'Open'

4. Then this wondow shows. Click on 'Options' tab, check the box 'Start up genome browser after loading the project', then click 'save and reload script'

Then click on 'Load'

5. Then this window shows, click on 'Set'

6. The program will start working and this window will come back for viewing.

Documentation

http://www.svaproject.org/