GATK

GATK is a software package for analysis of high-throughput sequencing 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.

Availability and Restrictions

Versions

The following versions of GATK are available on OSC clusters:

Version Owens Pitzer Note
3.5 X*    
4.0.11.0   X*  
4.1.2.0 X X  
* Current default version

You can use module spider gatk to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access for Academic Users

GATK4 is available to all OSC users under BSD 3-clause License.

GATK3 is available to academic OSC users who agree to the terms of the license agreement. Please review the license agreement carefully before use. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type

Broad Institute, Inc., BSD 3-clause License (GATK4 only)

Usage

Usage on Owens

Set-up

To configure your environment for use of GATK, run the following command: module load gatk. The default version will be loaded. To select a particular GATK version, use module load gatk/version. For example, use module load gatk/4.1.2.0 to load GATK 4.1.2.0.

Usage

This software is a Java executable .jar file; thus, it is not possible to add to the PATH environment variable. From module load gatk, a new environment variable, GATK, will be set. Thus, users can use the software by running the following command: gatk {other options},e.g  run gatk -h to see all options.

Usage on Pitzer

Set-up

To configure your environment for use of GATK, run the following command: module load gatk. The default version will be loaded.

Usage

This software is a Java executable .jar file; thus, it is not possible to add to the PATH environment variable. From module load gatk, a new environment variable, GATK, will be set. Thus, users can use the software by running the following command: gatk {other options},e.g  run gatk -h to see all options.

Known Issues

CBLAS undefined symbol error

Update: 05/22/2019 
Version: all

If you use GATK tools that need CBLAS (e.g. CreateReadCountPanelOfNormals), you might encounter an error as

INFO: successfully loaded /tmp/jniloader1239007313705592313netlib-native_system-linux-x86_64.so
java: symbol lookup error: /tmp/jniloader1239007313705592313netlib-native_system-linux-x86_64.so: undefined symbol: cblas_dspr
java: symbol lookup error: /tmp/jniloader1239007313705592313netlib-native_system-linux-x86_64.so: undefined symbol: cblas_dspr

The error raises because the system-default LAPACK does not support CBLAS.  The remedy is to run GATK in conjunction with lapack/3.8.0:

$ module load lapack/3.8.0
$ module load gatk/4.1.2.0
$ LD_LIBRARY_PATH=$OSC_LAPACK_DIR/lib64 gatk AnyTool toolArgs

Alternatively, we recommend using the GATK container. First, download the GATK container to your home or project directory

$ qsub -I -l nodes=1:ppn=1
$ cd $TMPDIR
$ export SINGULARITY_CACHEDIR=$TMPDIR
$ SINGULARITY_TMPDIR=$TMPDIR 
$ singularity pull docker://broadinstitute/gatk:4.1.2.0
$ cp gatk_4.1.2.0.sif ~/

Then run any GATK tool via

$ singularity exec ~/gatk_4.1.2.0.sif gatk AnyTool ToolArgs

You can read more about container in general from here. If you have any further questions, please contact OSC Help.

Further Reading

Supercomputer: 
Service: 
Fields of Science: