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?