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Table 4 Financial costs per sample when running an optimized pipeline, based on AWS on-demand pricing as of August 2019: c5.9xlarge at $1.53 per hour and c5.18xlarge at $3.06 per hour

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

GATK versionSplittingSamplesNodesWalltime, hrsc5.9xlargec5.18xlarge
GATK 4.0.1.2no splitting1120.7$31.7$63.3
GATK 3.8no splitting1115.3$23.4$46.8
GATK 3.812 chunks143.4$20.8$41.6
GATK 3.86 chunks124.7$14.4$28.8
GATK 3.816 chunks115.0$7.7$15.3
GATK 4.0.1.216 chunks113.6$5.5$11.0
GATK 4.0.1.2no splitting40134.1$1.3$2.6
  1. Configurations are sorted by cost.