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.
Runtime Performance of UnifiedGenotyper slows down with increasing Thread size?
I have run GATK's UnifiedGenotyper tool with different thread sizes (9, 18, 36 on a 40-core machine) in order to see how well it scales for an increasing thread size. I first tried out UnifiedGenotyper of version 1.7 and set -nt to 9, 18, and 36 with 8GB heap assigned for a 88GB large BAM file, respectively.
When looking at the results, I noticed that runtime performance increased when using more threads, so I updated GATK to version 2.7-4 in order to check if this behavior has vanished with the newer version.
I also noticed then that there exists another thread-parameter for the number of cpu threads.
So, I ran GATK's UnifiedGenotyper version 2.7-4 for a 88GB large file on a 40-core linux machine with -nt 1, -nct 9/18/36, and assigned 8GB heap.
The behavior in runtime performance remained the same. What am I missing here?