GVAF: Generalized, flexible filtering software for annotated variant files
GVAF can be used to perform the following functions on annotated files.
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Convert from the VCF derived genotype data to user-friendly genotype-related fields.
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Add the fields including further information about the variant.
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Filter out variants using simple but flexible filtering expression.
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Export output files with customized file format.
This program consists of two parts, user interface tools (written bash script) and an executable jar file. The user interface tools is used for handling the user requests, whereas a executable jar file provides the main function for manipulating the genetic variants on annotated files.
System Requirements
The program in this page was developed and tested on Java version 1.7.0, and require Java virtual machine 1.7.0 or higher.
Installing GVAF
GVAF can be installed as follows:
1. Download a file
2. Decompress the downloaded file into a work directory.
# Unzip downloaded file <downloaded file path>
unzip GVAF.zip
3. Set configuration on your computer.
# Go to GVAF directory
cd GVAF
# Check the path of GVAF direcory using "pwd" command
pwd
/home/tools/GVAF
# Adding your GVAF directory to PATH (for example, "~/.bash_profile") like the followings
export GVAF_HOME="/home/tools/GVAF"
export PATH=$GVAF_HOME/scripts:$PATH
# Update PATH information if necessary, for example as follows:
source ~/.bash_profile
4. Change permission of UI
# Go to the GVAF scripts directory
cd scripts
# Grant executable permission for UI
chmod 755 *
Documentation
The GVAF manual document includes the following information:
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A detailed description of the main functions.
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Available options of user interface tools.
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Several examples for manipulating the variants of annotated files using the main functions.
The GVAF manual document:
Downloads
The GVAF file consisting of GVAF program and user interface tools:
The dummy data mentioned in all examples of the GVAF manual document:
Availability and License
GVAF is freely available to non-commercial users. Contact the developer (sjung@gachon.ac.kr) for the license of commercial purposes.