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.