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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.
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Understanding -nct and -nt
I am trying to understand GATK's parameters for parallelism:
-nt / --num_threads controls the number of data threads sent to the processor
-nct / --num_cpu_threads_per_data_thread controls the number of CPU threads allocated to each data thread
So, is the following example true?
-nt 8 means you use 8 cores
-nct 8 means you use 8 threads within a single core