GATK-Teaching: Difference between revisions
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=== Version === | === Version === | ||
3. | 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 | "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. | 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 load the module with | To use this version, please load the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
ml GATK/3. | ml GATK/3.8-0-Java-1.8.0_144 | ||
</pre> | </pre> | ||
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cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml GATK/3. | ml GATK/3.8-0-Java-1.8.0_144<br> | ||
java-jar$EBROOTGATK/GenomeAnalysisTK.jar <u>[options]</u><br> | java-jar$EBROOTGATK/GenomeAnalysisTK.jar <u>[options]</u><br> | ||
</div> | </div> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml GATK/3. | ml GATK/3.8-0-Java-1.8.0_144 | ||
java-jar$EBROOTGATK/GenomeAnalysisTK.jar -h | java-jar$EBROOTGATK/GenomeAnalysisTK.jar -h | ||
sh: java-jar/usr/local/apps/eb/GATK/3. | sh: java-jar/usr/local/apps/eb/GATK/3.8-0-Java-1.8.0_144/GenomeAnalysisTK.jar: No such file or directory | ||
</pre> | </pre> | ||
Revision as of 12:20, 15 August 2018
Category
Bioinformatics
Program On
Teaching
Version
3.8-0
Author / Distributor
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 load 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 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
#SBATCH --error=GATK.%j.err
cd $SLURM_SUBMIT_DIR
ml GATK/3.8-0-Java-1.8.0_144
java-jar$EBROOTGATK/GenomeAnalysisTK.jar [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 java-jar$EBROOTGATK/GenomeAnalysisTK.jar -h sh: java-jar/usr/local/apps/eb/GATK/3.8-0-Java-1.8.0_144/GenomeAnalysisTK.jar: No such file or directory
Installation
Source code is obtained from GATK
System
64-bit Linux