Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Is there any speed benefit to redirecting Djava.io.tmpdir 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 -Djava.io.tmpdir 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.