support:hpc:software:gatk
Genomics Analysis ToolKit
The Genomics Analysis Toolkit is located in /share/apps/gatk-1.4.37 on the bigmem nodes.
An example of a single GATK job
#!/bin/bash
### Change to the current working directory:
#$ -cwd
### Job name:
#$ -N SomeJobName
#$ -S /bin/bash
java -jar /share/apps/gatk-1.4.37/dist/GenomeAnalysisTK.jar -R exampleFASTA.fasta -I exampleBAM.bam \
-T CountReads -et NO_ET
support/hpc/software/gatk.txt · Last modified: 2012/03/09 13:42 by tlknight
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