GVAF: A command line-based software for manipulating germline

            variants on 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. 

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 1.8.0, and require Java virtual machine 1.7.0 or higher. 

 

Installing GVAF 

GVAF can be installed as follows: 

 

1. Download a file

 

    # Go to home directory

    cd

 

    # Download GVAF 

    wget -O GVAF.zip https://sites.google.com/site/sjunggsm/GVAF.zip?attredirects=0&d=1

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

    # Copy GVAF direcory using "pwd" command

    pwd 

    /home/tools/GVAF

    # Append the following lines into "~/.bash_profile"

    export GVAF_HOME="/home/tools/GVAF"

    export PATH=$GVAF_HOME/scripts:$PATH
 

    # Update "~/.bash_profile"

    source ~/.bash_profile

4. Change permission of UI

    # Go to scripts directory 

    cd scripts

    # Grant executable permission for UI

    chmod 755 *

 

Documentation

The GVAF manual document is included as follows: 

  • 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. 

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: