Example scripts for benchmarking the computational performance of GATK3.8 and GATK4.
Baseline The baseline files represent original tests of GATK3.8 and the newest release of GATK4 at the time of testing, GATK4.0.1.2.
Optimal The optimal files represent tests run with optimized parameters on GATK3.8 and GATK4.0.1.2.
Split The split file shows an example of splitting a WGS sample into chunks for parallel processing with GATK4.0.1.2 (which does not have multithreading capabilities).
For more information on tests, parameters, and system specifications, please see our pre-print https://www.biorxiv.org/content/10.1101/348565v1.