Table 5 Performance impact of PairHMM library with heap memory implementation in the GATK 3.3 HaplotypeCaller.
From: Accelerating next generation sequencing data analysis with system level optimizations
Benchmarking case study name | PairHMM library | Heap memory prerequisite | Committed heap memory | CPU utilization | HaplotypeCaller execution time (in hours) |
|---|---|---|---|---|---|
Without PairHMM and No heap memory | No | 0 GB | 14.3 GB | upto 40% | 2.51 |
Without PairHMM and with heap memory | No | 128 GB | 48.5 GB | upto 73% | 2.34 |
With PairHMM and No heap memory | Yes | 0 GB | 12 GB | upto 58% | 1.18 |
With PairHMM and with heap memory | Yes | 128 GB | 50.3 GB | upto 72% | 0.912 |
