GATK is a Toolkit for Genome Analysis
More specifically, it's a toolkit for variant discovery.
The GATK is the industry standard for identifying SNPs and indels
in germline DNA and RNAseq data, and its scope is currently being
extended to include somatic variant calling tools. In addition to
the variant callers themselves, the GATK also includes many utilities
to perform related tasks such as processing and quality control of
high-throughput sequencing data.
GATK-Queue is command-line scripting framework for defining multi-stage
genomic analysis pipelines combined with an execution manager that
runs those pipelines from end-to-end.
* Get started/GATK Homepage
* GATK documentation/BPR
* A primer on parallelism with the GATK(-Queue)
* GATK repository (binaries/sources)
* bwHPC examples can be found here:
Please read the 'README.bwhpc-examples' file.
Please use the 'gatk' wrapper to start the programm.
Beware: The 'GenomeAnalysisTK-3.5.jar' file can't be started
without an absolute path. Appending $HOME to $GATK_HOME will _not_
start the *.jar.
But the gatk-wrapper works fine.
In case of problems, please contact: bwhpc (at) uni-konstanz.de
This module is available for all users.