GATK-Teaching: Difference between revisions

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=== Version ===
=== Version ===
3.4-0
3.8-0
   
   
=== Author / Distributor ===
=== Author / Distributor ===
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=== Description ===
=== Description ===
"The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute   to analyse next-generation resequencing data. The toolkit offers a wide variety of tools,  with a primary focus on variant discovery and genotyping as well as strong emphasis on   data quality assurance. Its robust architecture, powerful processing engine and   high-performance computing features make it capable of taking on projects of any size."
"The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools,  with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size."
More details are at [http://www.broadinstitute.org/gatk/ GATK]
More details are at [http://www.broadinstitute.org/gatk/ GATK]


=== Running Program ===
=== Running Program ===


The last version of this application is at /usr/local/apps/eb/GATK/3.4-0-Java-1.8.0_144
The last version of this application is at /usr/local/apps/eb/GATK/3.8-0-Java-1.8.0_144


To use this version, please loads the module with
To use this version, please loads the module with
<pre class="gscript">
<pre class="gscript">
ml GATK/3.4-0-Java-1.8.0_144
ml GATK/3.8-0-Java-1.8.0_144  
 
gatk
</pre>  
</pre>  


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cd $SLURM_SUBMIT_DIR<br>
cd $SLURM_SUBMIT_DIR<br>
 
ml GATK/3.8-0-Java-1.8.0_144<br>  
ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> <u>[options]</u><br>   
gatk <u>[options]</u><br>   
</div>
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values or be reviewed .   
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.   


Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.
Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.
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<pre  class="gcommand">
<pre  class="gcommand">
GATK/3.4-0-Java-1.8.0_144
ml GATK/3.8-0-Java-1.8.0_144  
gatk -h
gatk gatk -h


</pre>
</pre>

Revision as of 10:33, 10 August 2018

Category

Bioinformatics

Program On

Teaching

Version

3.8-0

Author / Distributor

GATK

Description

"The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size." More details are at GATK

Running Program

The last version of this application is at /usr/local/apps/eb/GATK/3.8-0-Java-1.8.0_144

To use this version, please loads the module with

ml GATK/3.8-0-Java-1.8.0_144 

Here is an example of a shell script, sub.sh, to run on at the batch queue:

#!/bin/bash
#SBATCH --job-name=j_GATK
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=GATK.%j.out

cd $SLURM_SUBMIT_DIR
ml GATK/3.8-0-Java-1.8.0_144
gatk [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.


Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml GATK/3.8-0-Java-1.8.0_144 
gatk gatk -h

Back to Top

Installation

Source code is obtained from GATK

System

64-bit Linux