GATK -Xmx4G and -Xmx8G

Question

[lovegenetics]

Dear all,

I would like to know what the difference is between the "-Xmx4G" and "-Xmx8G" switches on GATK. All I know is, both of these switches are used for specifying memory allocation (which I'm still not quite sure I understand the meaning of it) from https://software.broadinstitute.org/gatk/documentation/article?id=11050.

I want to use the HaplotypeCaller tool on my bam files, and I'd like to know the difference between switches before I proceed.

Many thanks

Reem.

Answer 1

[andrew.j.skelton73]

These aren't GATK specific switches, but a java JVM (java virtual machine) parameter. Since GATK4, these parameters have been absorbed into the main binary to integrate well with the WDL notation and Cromwell orchestration.

-Xmx is the switch to tell Java how much memory it's allowed to work with (heap size). This is akin to the amount of RAM on your machine. -Xmx8G means that you're telling Java it can work with 8GB of memory (or RAM) on your machine. It's important not to allocate more than your machine has available.

[lovegenetics]

Thanks alot, Andrew.