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GVAF: Generalized, flexible filtering software for annotated variant files

GVAF can be used to perform the following functions on annotated files. 

  • Convert from the VCF derived genotype data to user-friendly genotype-related fields.

  • Add the fields including further information about the variant. 

  • Filter out variants using simple but flexible filtering expression.

  • Export output files with customized file format. 

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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. 

 

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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. 

 

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Installing GVAF 

GVAF can be installed as follows: 

 

1. Download a file

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2. Decompress the downloaded file into a work directory.

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    # Unzip downloaded file <downloaded file path>

    unzip GVAF.zip 

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3. Set configuration on your computer.

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    # Go to GVAF directory

    cd GVAF

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    # Check the path of GVAF direcory using "pwd" command

    pwd 

    /home/tools/GVAF

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    # 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

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4. Change permission of UI

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    # Go to the GVAF scripts directory 

    cd scripts

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    # Grant executable permission for UI

    chmod 755 *

 

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Documentation

The GVAF manual document includes the following information: 

  • A detailed description of the main functions.

  • Available options of user interface tools. 

  • Several examples for manipulating the variants of annotated files using the main functions. 

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The GVAF manual document: 

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Downloads

The GVAF file consisting of GVAF program and user interface tools: 

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The dummy data mentioned in all examples of the GVAF manual document: 

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Availability and License

GVAF is freely available to non-commercial users. Contact the developer (sjung@gachon.ac.kr) for the license of commercial purposes.

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