GATK 4.1.5.0-GCCcore-9.3.0-Java-11

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.

Accessing GATK 4.1.5.0-GCCcore-9.3.0-Java-11

To load the module for GATK 4.1.5.0-GCCcore-9.3.0-Java-11 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load GATK/4.1.5.0-GCCcore-9.3.0-Java-11

BEAR Apps Version

2020a

Architectures

EL8-cascadelake — EL8-haswell — Ubuntu20.04-haswell

The listed architectures consist of two part: OS-CPU.

  • BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
  • BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.

More Information

For more information visit the GATK website.

Dependencies

This version of GATK has a direct dependency on: GCCcore/9.3.0 Java/11 Python/2.7.18-GCCcore-9.3.0 Python/3.8.2-GCCcore-9.3.0

This version of GATK is compatible with multiple vesions of Python. At any time, only one of the versions of Python can be active and the desired version of Python should be loaded before loading this version of GATK.

Required By

This version of GATK is a direct dependent of: DROP/1.0.3-foss-2020a-Python-3.8.2-R-4.0.0

Other Versions

These versions of GATK are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 18th March 2021