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.
CNNScoreVariants, too much threads
in the BestPractice workflows you advise to use HaplotypeCaller with the "-XX:GCTimeLimit=50" and "-X:GCHeapFreeLimit=10" java options.
Is there something similar for CNNScoreVariants? I tried to use several java options with different values to limit threads but it is quite impossible. Without any option I have 116 threads, running only one command, with 5 java options I can limit them to 95 ... still too much! What should I limit here?