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GATK: Difference between revisions
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As you probably notice, there are some arguments to be passed directly to java through the '''--java-options''' such as the maximum heap memory ('''-Xmx8G''' in the example, reserving 8 Gb of memory for the virtual machine). We recommend that you '''always''' use '''-DGATK_STACKTRACE_ON_USER_EXCEPTION=true''' since it will give you more information in case the program fails. This information can help you or us (in case you needed support) to solve the issue. | As you probably notice, there are some arguments to be passed directly to java through the '''--java-options''' such as the maximum heap memory ('''-Xmx8G''' in the example, reserving 8 Gb of memory for the virtual machine). We recommend that you '''always''' use '''-DGATK_STACKTRACE_ON_USER_EXCEPTION=true''' since it will give you more information in case the program fails. This information can help you or us (in case you needed support) to solve the issue. | ||
Note that all options passed to '''--java-options''' have to be within quotation marks | Note that all options passed to '''--java-options''' have to be within quotation marks. | ||
===Earlier versions than GATK 4 === | |||
Earlier versions of GATK do not have the '''gatk''' command. Instead, one has to call the jar file: | |||
<pre> | |||
java -jar GenomeAnalysisTK.jar PROGRAM OPTIONS | |||
</pre> | |||
However, GenomeAnalysisTK.jar must be in PATH. In Compute Canada systems, the environmental variables '''$EBROOTPICARD''' for Picard (included in GATK >= 4) and '''$EBROOTGATK''' for GATK contain the path to the jar file, so the appropriate way to call GATK <= 3 is: | |||
<pre> | |||
module load gatk/3.8 | |||
java -jar java -jar $EBROOTGATK/GenomeAnalysisTK.jar PROGRAM OPTIONS | |||
</pre> | |||
You can find the specific usage of GATK <= 3 in the [https://gatkforums.broadinstitute.org/gatk/categories/gatk-guide GATK3 guide]. | |||
==Frequently asked questions == | ==Frequently asked questions == | ||