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Table 1 Effects of asynchronous I/O settings on walltime (hours) in GATK4

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

 

Async I/O activated?

Tool Name

no

all

only for samtools I/O

BaseRecalibrator

4.07

2.95

2.88

ApplyBQSR

2.38

2.07

2.08

HaplotypeCaller

17.25

17.31

17.08

  1. Sample: NA12878 WGS.
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BMC Bioinformatics

ISSN: 1471-2105

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