Fig. 4

Resource consumption of the basic workflow with increasing optimization levels. a CPU and memory utilization of the entire workflow, using a single interval (comprising the entire genome) for the HaplotypeCaller and without any Java optimization (total runtime: 67.1 h)). Four phases can be distinguished within the workflow (separated by dashed lines), that are dominated by individual applications. b When the genome is split into six separate intervals for the HaplotypeCaller analysis, but without any Java optimization (41.4 h). c With optimized Java garbage collection for each GATK application (39.8 h). d With optimized Java settings (garbage collection and heap size) for all GATK applications and four default threads for the native pairHMM algorithm of the HaplotypeCaller (40.3 h). e When all optimizations are applied to the workflow, including six parallel intervals for variant calling by the HaplotypeCaller, a single hmmThread for each HaplotypeCaller, and all Java optimizations (garbage collection and heap size) (34.7 h)