Attention
GPU users: GPU nodes run EL9, while this documentation still reflects the EL7 software stack.
Run module avail on an EL9 login node, or within an interactive session on the relevant GPU type, to see the software available.
The documentation will be updated once all nodes have migrated to EL9.
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.
Note
This is an autogenerated page, more detail including examples may be available for this package. Please see the first section of Software on Stanage
After connecting to Stanage (see Establishing a SSH connection), start an interactive session with the following command:
srun --pty bash -i
A version of GATK can then be made available with one of the following:
module load GATK/4.3.0.0-GCCcore-11.3.0-Java-11
Notes
GATK was installed using Easybuild, build details can be found in $EBROOTGATK/easybuild with a given module loaded.