Skip to main content
Fig. 4 | BMC Bioinformatics

Fig. 4

From: Recommendations for performance optimizations when using GATK3.8 and GATK4

Fig. 4

Effects of data-level parallelization in GATK3.8. Sample: NA12878 WGS. The “Baseline” was a naive approach where we gave each tool 40 threads (1 thread per core). The “Baseline Optimized” gave each tool 40 threads, except for PrintReads, which utilized 3 threads. MarkDuplicates and BaseRecalibrator were given 2 and 20 parallel garbage collection threads, respectively. “Split 2,” “Split 3,” etc. means that the aligned sorted BAM was split into 2, 3, etc. chunks, as shown in Table 2. Panel (a) shows experiments with chunks computing on the same node. In panel (b) computation was spread across nodes in groups of 3 chunks per node

Back to article page