Fig. 3

Influence of different Java heap sizes on the resource utilization of individual GATK applications. Besides the number of Java garbage collection threads, the provided heap size has a considerable impact on the performance of some GATK applications. Again, the four tools SortSam, MarkDuplicates, HaplotypeCaller and GatherVcfs (see columns) (GATK version 4.1.9) were assessed for their respective resource usage in terms of wall time, system time and memory usage (see rows). The intention was to identify Java heap sizes that result in minimized resource utilization. Therefore, lower readings on the ordinate are preferable as they reflect lower resource consumption of the respective application. Triplicate measurements were recorded for each of ten different values for Java heap size (1, 2, 4, 6, 8, 12, 16, 24, 32 and 48 Gb) and resulting mean values plotted in lines. The gray line in the resident set size plots indicate parity between the maximum allowed heap size and the actual memory usage. All measurements were recorded with two garbage collection threads enabled. As in Fig. 2, different scales of the ordinates of each plot have to be taken into account, since they vary considerably between the individual plots. In additon, the HaplotypeCaller was again limited to the analysis of chromosome 6 (NC_006093.5)