Is there any speed benefit to redirecting to local scratch?

I'm currently putting together a workflow for WGS (Illumina 30x) variant calling (HaplotypeCaller) using GATK 3.2 on our local SGE grid. I was wondering whether there is any speedup with redirecting to scratch space on the local node? Which steps are I/O intensive and could potentially benefit from this? Currently the bottleneck seems to be IndelRealigner which takes ~14hrs.
Thank you.


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