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 and 3.7. Freely available to users.
Own licence freely available for academic users.
Example of environment initialization:
module add gatk-2.7.2
module add gatk-3.7
Initialization makes available also java 7 (or java 8 for version 3.7) and system variable $GATK pointing into GATK install dir. Usage of one of the tools with sample data:
java -Xmx2g -jar $GATK/GenomeAnalysisTK.jar -T CountReads -R $GATK/resources/exampleFASTA.fasta -I $GATK/resources/exampleBAM.bam
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/ .