java queue GATK_GATK queue(2)

Queue itself just generates a queue of jobs; you still need to dispatch them using a job manager/scheduler like LSF.

Compare and combine

So you see, scatter-gather is a very different process from multi-threading because the parallelization happens outside of the program itself. The big advantage is that this opens up the upper level of computing: the cluster level. Remember, the GATK program is limited to dispatching threads to the processor of the machine on which it is run – it cannot by itself send threads to a different machine. But Queue can dispatch scattered GATK jobs to different machines in a computing cluster by interfacing with your cluster's job management software.

That being said, multithreading has the great advantage that cores and machines all have access to shared machine memory with very high bandwidth capacity. In contrast, the multiple machines on a network used for scatter-gather are fundamentally limited by network costs.

The good news is thatyou can combine scatter-gather and multithreading: use Queue to scatter GATK jobs to different nodes on your cluster, then use the GATK's internal multithreading capabilities to parallelize the jobs running on each node.