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Table 1 The runtime for each step of HaplotypeCaller [6]

From: ADS-HCSpark: A scalable HaplotypeCaller leveraging adaptive data segmentation to accelerate variant calling on Spark

Stage

Runtime

Percentage

Assembly

2598 s

13%

PairHMM

14,225 s

70%

Traversal + Genotyping

3379 s

17%