SOFT : GATK
------
Site du soft: https://gatk.broadinstitute.org/hc/en-us
-------------

LICENSE:
--------

-->  Version v3.8-0

FOR-PROFIT PURPOSES: If you plan to use GATK in any for-profit application, you are required to purchase a license. To do so, please contact softwarelicensing@broadinstitute.org to discuss your application with our license manager.
ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES: Under this license, you can use the program and view the source code for free as long as you are using GATK strictly for non-profit purposes. The full text of this license is included below. If your usage qualifies for this license, you can download the program and start using it right away.

https://software.broadinstitute.org/gatk/download/licensing

--> Version > v4.0.0.0
Apache 2.0 license. https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT

See software documentation for more informations.

Location: /usr/local/bioinfo/src/GATK
---------

Load binaries and environment:
------------------------------

-> Version v3.8-0

$ module load bioinfo/GATK/3.8-0
$ java -jar $GATK_HOME/GenomeAnalysisTK.jar -h

-> Version v3.8-1

$ module load bioinfo/GATK/3.8-1
$ java -jar $GATK_HOME/GenomeAnalysisTK.jar -h

-> Version v4.2.0.0

# Need Python3, Java17
module load devel/python/Python-3.11.1 devel/java/17.0.6

module load bioinfo/GATK/4.2.0.0

-> Version v4.2.6.1

# Need Python3, Java17
module load devel/python/Python-3.11.1 devel/java/17.0.6

module load bioinfo/GATK/4.2.6.1


-> Version v4.4.0.0

# Need Python3, Java17 
module load devel/python/Python-3.11.1 devel/java/17.0.6

module load bioinfo/GATK/4.4.0.0

-> Version v4.6.2.0

module load devel/python/Python-3.11.1 devel/java/17.0.6 statistics/R/4.3.1 

module load bioinfo/GATK/4.6.2.0


Example directory for use on cluster:
-------------------------------------

/usr/local/bioinfo/src/GATK/example_on_cluster

To submit: sbatch test_gatk-4.4.0.0.sh 

See software documentation and our FAQ (http://bioinfo.genotoul.fr/index.php/faq/) for more informations.


Example directory for use on cluster:
-------------------------------------

/usr/local/bioinfo/src/GATK/example_on_cluster

To submit: sbatch test_gatk-4.6.2.0.sh 

See software documentation and our FAQ (http://bioinfo.genotoul.fr/index.php/faq/) for more informations.