GenomeAnalysisTK (GATK)

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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.

Availability

Versions 2.7-2 and 3.7. Freely available to users.

Available modules:

gatk-2.7.2
gatk-3.7

Licence

Own licence freely available for academic users.

Use

Example of environment initialization:

module add gatk-2.7.2

or

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

Documentation

Dokumentation is available at http://www.broadinstitute.org/gatk/guide/ .

Program manager

meta@cesnet.cz

Homepage

http://www.broadinstitute.org/gatk