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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 version

Splitting

Samples

Nodes

Walltime, hrs

c5.9xlarge

c5.18xlarge

GATK 4.0.1.2

no splitting

1

1

20.7

$31.7

$63.3

GATK 3.8

no splitting

1

1

15.3

$23.4

$46.8

GATK 3.8

12 chunks

1

4

3.4

$20.8

$41.6

GATK 3.8

6 chunks

1

2

4.7

$14.4

$28.8

GATK 3.8

16 chunks

1

1

5.0

$7.7

$15.3

GATK 4.0.1.2

16 chunks

1

1

3.6

$5.5

$11.0

GATK 4.0.1.2

no splitting

40

1

34.1

$1.3

$2.6

  1. Configurations are sorted by cost.