Genome Analysis Toolkit

module avail gatk/

Genome Analysis Toolkit is a generic tool for pairwise sequence comparison. It allows you to align sequences using many alignment models, either exhaustive dynamic programming or a variety of heuristics.

Usage

In the qsub command, it is necessary to specify the parameter ompthreads to allow a run on multiple threads, e.g. (for eight threads):

qsub -l select=1:ncpus=8:ompthreads=8:mem=...

Versions 4.X

GATK 4 has a wrapper script, gatk, which significantly simplifies commands.

gatk --help    # to print help
gatk --list    # to list all available tools inside the toolkit

An example of a command with data:

gatk --java-options "-Xmx20G" HaplotypeCaller -R reference.fasta -I input.bam -O output.vcf

The -Xmx memory option represents the amount of memory used only by the java process. However, the user must request more memory from PBS to cover all other processes outside of java. For example, for -Xmx20g, reserve mem=30gb from PBS.

Versions 3.X and 2.X

Initialization also makes java/opendjk and system variable $GATK available pointing into the GATK install directory. Usage of one of the tools with sample data (not for version 3.8-0):

java -Xmx20g -jar "$GATK"/GenomeAnalysisTK.jar -T CountReads -R "$GATK"/resources/exampleFASTA.fasta -I "$GATK"/resources/exampleBAM.bam

During large data processing, some problems with the size of the tmp directory can occur (and can lead to the end of a job or a significant slowdown). In this case, add the parameter -Djava.io.tmpdir="${SCRATCHDIR}"/tmp into the java command.

List of tools and version check:

java -jar "$GATK"/GenomeAnalysisTK.jar --help
java -jar "$GATK"/GenomeAnalysisTK.jar --version