1ba045f4_he_GATK___RETIRED___GATK_Forum__Shared_Memory
[Property] How to enable [Scatter/Gather] 1. Provide -L interval lists to the GATK; a different one for each of the N independent GATK tools. For example -L chr1 for first process, and -L chr2 for the second. When all processes have finished, merge the output together, as appropriate (e.g. use MergeSam.jar for BAMs, and cat or CombineVariants for VCFs). 2. Use GATK-Queue to automatically divide up your GATK jobs. For example, using this.scatterCount = 10 argument will result in 10 independent processes. [Shared Memory] 
Use the -nt argument in the Engine, on any walker that supports shared memory parallelism (the engine will tell you if it does not).
Parallelism with the GATK - RETIRED - GATK-Forum
Shared Memory