Monday, January 18, 2016

VCFtools and Tabix installation on Linux (RHEL)

VCFtools installation

Download vcftools from here:
 Unzip the downloaded package and proceed to install RHEL packages required to build vcftools using the following:


yum install autoconf
yum install automake
yum install gcc
yum group install “Development Tools”
yum install zlib
yum install zlib-devel

export PERL5LIB=/path/to/your/vcftools-directory/src/perl/
cd vcftools/
make install

The binary executables will be installed in the /usr/local/bin folder.
To add the executables to your path use the following:
export PATH=$PATH:/usr/local/bin

To set it permanently add the following line to the /etc/profile file just before it gets exported:

Tabix installation

(1) Go here to download the newest release.

(2) Extract the file:

tar xvjf tabix-0.2.6.tar.bz2

(3) Compile the program by typing make on the UNIX command line.
(4) Export the path by adding the following line to your .bashrc file, saving your .bashrc file, and typing source on the UNIX command line.  Note: path_to_tabix is the directory where tabix is installed.

export PATH=$PATH:/path_to_tabix/tabix-0.2.6