Phen-Gen standalone

Our standalone (Version 1.0) is available under the GNU General Public License. It has been tested in Linux environment (Ubuntu 12.04.3 LTS, CentOS 6.1, and RHEL 6.1).

To install the standalone:

  1. Check that Perl is already installed: type perl -v on the command line. If it's not available, click here to install it.
  2. Download the standalone. (Size 2.9 GB)
  3. Transfer the downloaded file to the directory where you want to run it (e.g. /home/yourusername/phengen).
  4. To decompress and extract the contents of the standalone: tar -zxvf Phen-GenV1.tar.gz

To run the standalone:

Execute the command:
perl input_phenotype=< text > input_vcf=< vcf > input_ped=< ped > inheritance=< i > predictor=< p > stringency=< s > discard_de_novo=< d >

Please refer to README.txt for a description of the command line and its parameters, and file formats. The approximate run time is 15 minutes.

If you have any questions on how to install/run the software, kindly contact us.