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 | Cardinal | Notes |
|---|---|---|---|---|
| 3.5 | X | |||
| 4.0.11.0 | X | |||
| 4.1.2.0 | X* | X* | ||
| 4.4.0.0 | X | X | ||
| 4.6.0.0 | X* |
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. 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
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
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
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.
