VarGenius - Variant Discovery and Annotation Tool Copyright (C) <2018>
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
VarGenius is a pipeline for the detection and annotation of genetic variants. It can be currently used with WES and targeted sequencing.
To start using VarGenius you must follow the instructions into the GUIDE folder. There you will find additional information on the content of the User Guide.
- The install and go section is here: INSTALL. There you will also learn how to install VarGenius;
- After you install you can try to run the pipeline for the first time. Few settings are needed before to run. Please follow instructions from the TUTORIAL.
Please enjoy this product and send us questions and suggestions!
To work, VarGenius needs:
- PostgreSQL database
- Perl
- BioPerl
- R
- samtools
- picard
- GATK
- BWA
- TrimGalore
- FastQC
- bedtools
- Annovar
Check for the tested versions in the INSTALL page.
VarGenius can be used only with a PBS cluster. It has been desigend to create jobs with the qsub command. The execution time depends strongly from the speed and memory of your machine.
The pipeline needs around 5 hours to run the complete sequence of tasks. Depending by the queue and resources used by other users of the cluster, jobs will wait less or more time.
The space needed to build the PosgreSQL database depends from the number of variants contained. 100 samples (WES and targeted) consisting of 300 thousands variants use around 4GB of disk space.
The space needed for all the default databases of Annovar takes 1.2 Terabyte in our system
If you get some error during the installation or the running of VarGenius please see the FAQ page of the user guide or ask on the google group: https://groups.google.com/forum/#!forum/VarGenius