GATK-Teaching
Category
Bioinformatics
Program On
Teaching
Version
3.4-0
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/3.4-0-Java-1.8.0_144
To use this version, please load the module with
ml GATK/3.4-0-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 $SLURM_SUBMIT_DIR
ml GATK/3.4-0-Java-1.8.0_144
java-jar$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/3.4-0-Java-1.8.0_144 java-jar$EBROOTGATK/GenomeAnalysisTK.jar -h sh: java-jar/usr/local/apps/eb/GATK/3.4-0-Java-1.8.0_144/GenomeAnalysisTK.jar: No such file or directory
Installation
Source code is obtained from GATK
System
64-bit Linux