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.
Versions 2.7.2, 3.7, 3.8-0, 220.127.116.11, 18.104.22.168 and 22.214.171.124 are freely available to users.
First, you have to prepare your environment by executing:
module load gatk-126.96.36.199
GATK 4 version has a wrapper script gatk, which significantly simplifies commands. Now, you can just run
gatk --help # to print help gatk --list # to list of all available tools inside the toolkit
to get a list of all available tools in the toolkit. This is the basic structure of invocation of a tool named
gatk [--java-options "jvm args like -Xmx4G go here"] ToolName [GATK args go here]
This is how a command might look like in real world:
gatk -Xmx8G HaplotypeCaller -R reference.fasta -I input.bam -O output.vcf
If you are not familiar with this syntax, please see the official Quick Start tutorial.
Version 3.8-0 and older
Example of environment initialization:
module add gatk-2.7.2
module add gatk-3.7
module add gatk-3.8-0
Initialization makes available also java 7 (or java 8 for version 3.7 and 3.8) and system variable $GATK pointing into GATK install dir. Usage of one of the tools with sample data (not for version 3.8-0):
java -Xmx2g -jar $GATK/GenomeAnalysisTK.jar -T CountReads -R $GATK/resources/exampleFASTA.fasta -I $GATK/resources/exampleBAM.bam
During large data processing, some problems with size of tmp directory can occurs (and can lead to the end of job or significant slowdown). In this case, add parameter
List of tools and version check:
java -Xmx2g -jar $GATK/GenomeAnalysisTK.jar --help java -Xmx2g -jar $GATK/GenomeAnalysisTK.jar --version
Dokumentation is available at http://www.broadinstitute.org/gatk/guide/ .