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Fig. 1 | BMC Bioinformatics

Fig. 1

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

Fig. 1

GATK3.8 Thread Scalability. a Scalability of BaseRecalibrator, PrintReads and HaplotypeCaller. Sample: NA12878 WGS. Fold change refers to the fold difference in walltime between the new measurement when compared to the performance with a single thread ((newtimebaselinetime)/baselinetime). b Scalability of PrintReads, in more detail. Normally walltime should decrease with thread count, as the computation is performed in parallel by multiple threads. However, in the case of PrintReads the opposite is observed. The increasing walltime as a function of thread count therefore signifies poor scalability and explains the decreasing trend for PrintReads line on panel (a). Sample: NA12878 chr 21. Error bars denote 1 SD around the mean of three replicates

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