GATK
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.
https://www.broadinstitute.org/gatk/
Available modules
The overview below shows which GATK installations are available per target architecture in the HPCC module system, ordered based on software version (new to old).
To start using GATK, load one of these modules using a module load command like:
1 | |
(This data was automatically generated on Thu, 17 Apr 2025 at 12:00:12 EDT)
| neoverse_v1 | generic | zen2 | zen3 | zen4 | haswell | skylake_avx512 | |
|---|---|---|---|---|---|---|---|
| Grace Nodes | everywhere (except Grace nodes) | amd20 | amd22 | amd24 | intel16 | intel18,amd20-v100,amd21,intel21 | |
| GATK/4.5.0.0-GCCcore-12.3.0-Java-17 | - | x | - | - | - | x | - |
| GATK/4.3.0.0-GCCcore-12.3.0-Java-11 | - | x | - | - | - | - | - |