Protocol

WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1)

Wall-clock minutes for the HaplotypeCaller or DRAGEN GSVC calling stage on ten WGS samples, CPU-only versus Parabricks on three GPU types versus DRAGEN.

5 evaluations · 50 results

Overview

Wall-clock minutes for the HaplotypeCaller or DRAGEN GSVC calling stage on ten WGS samples, CPU-only versus Parabricks on three GPU types versus DRAGEN.

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5 recorded evaluations, 50 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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5 evaluations · 50 results. Different protocols are not a single leaderboard.

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Sources and history

Release 2026-10-09-8cc1db47c7f9 · Record review: source checked

2 source records and release history

Benchmarking accelerated next-generation sequencing analysis pipelines · Original source · Bioinformatics Advances 5(1):vbaf085, published 2025-05-15; PMC12092081 full-text XML
Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Original source · 'Publication-ready_Supplementary materials-20250404.pdf' inside vbaf085_supplementary_data.zip

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Technical metadata and extraction receipts

Stable ID: model-execution-20261009-protocol-samarakoon2025-hc

areas: dna-genomes
contexts: clinical_research
protocol: Variant calling with GATK or Parabricks HaplotypeCaller, or DRAGEN GSVC. Real (wall-clock) time measured per stage from FASTQ input (Methods 2.6).
version: Supplementary Table S3 sub-table 'b.1) Variant calling via HC or DRAGEN GSVC'
unit: minute
metric: runtime
limitations: One run per sample and configuration; no repeats or variance printed.; Hardware differs between columns (CPU cluster, two GCP VMs, an HPC GPU node and a DRAGEN server), so differences mix software and hardware.; CPU-only nodes were shared with other users; GCP VMs ran in a multi-tenant environment (Table S2 notes).
denominator: 10
missing metadata: replicates: reason: unreported
source locator: Supplementary Table S3, sub-table 'b.1) Variant calling via HC or DRAGEN GSVC'

Related records

Suggest a correction

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	614 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12778', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	557 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12812', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	756 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12829', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	603 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12843', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	1150 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12877', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	1110 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12878', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	1350 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12889', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	1290 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12890', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	1090 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12891', column 'CPU' (PDF page text)
Configuration: CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	1150 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPU-only best-practice pipeline on AMD EPYC 7702 (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12892', column 'CPU' (PDF page text)
Configuration: Illumina DRAGEN v4.2 on DRAGEN server V2 (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	7.84 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Illumina DRAGEN v4.2 on DRAGEN server V2, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12778', column 'DRAGEN' (PDF page text)
Configuration: Illumina DRAGEN v4.2 on DRAGEN server V2 (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	7.88 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Illumina DRAGEN v4.2 on DRAGEN server V2, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12812', column 'DRAGEN' (PDF page text)
Configuration: Illumina DRAGEN v4.2 on DRAGEN server V2 (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	12.1 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Illumina DRAGEN v4.2 on DRAGEN server V2, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12829', column 'DRAGEN' (PDF page text)
Configuration: Illumina DRAGEN v4.2 on DRAGEN server V2 (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	8.19 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Illumina DRAGEN v4.2 on DRAGEN server V2, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12843', column 'DRAGEN' (PDF page text)
Configuration: Illumina DRAGEN v4.2 on DRAGEN server V2 (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	22.9 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Illumina DRAGEN v4.2 on DRAGEN server V2, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12877', column 'DRAGEN' (PDF page text)
Configuration: Illumina DRAGEN v4.2 on DRAGEN server V2 (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	21.4 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Illumina DRAGEN v4.2 on DRAGEN server V2, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12878', column 'DRAGEN' (PDF page text)
Configuration: Illumina DRAGEN v4.2 on DRAGEN server V2 (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	23.8 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Illumina DRAGEN v4.2 on DRAGEN server V2, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12889', column 'DRAGEN' (PDF page text)
Configuration: Illumina DRAGEN v4.2 on DRAGEN server V2 (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	19.9 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Illumina DRAGEN v4.2 on DRAGEN server V2, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12890', column 'DRAGEN' (PDF page text)
Configuration: Illumina DRAGEN v4.2 on DRAGEN server V2 (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	22 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Illumina DRAGEN v4.2 on DRAGEN server V2, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12891', column 'DRAGEN' (PDF page text)
Configuration: Illumina DRAGEN v4.2 on DRAGEN server V2 (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	23.2 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Illumina DRAGEN v4.2 on DRAGEN server V2, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12892', column 'DRAGEN' (PDF page text)
Configuration: NVIDIA Parabricks on 4 NVIDIA A100 GPUs (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	5.42 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NVIDIA Parabricks on 4 NVIDIA A100 GPUs (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12778', column 'A100' (PDF page text)
Configuration: NVIDIA Parabricks on 4 NVIDIA A100 GPUs (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	4.75 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NVIDIA Parabricks on 4 NVIDIA A100 GPUs (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12812', column 'A100' (PDF page text)
Configuration: NVIDIA Parabricks on 4 NVIDIA A100 GPUs (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	8.58 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NVIDIA Parabricks on 4 NVIDIA A100 GPUs (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12829', column 'A100' (PDF page text)
Configuration: NVIDIA Parabricks on 4 NVIDIA A100 GPUs (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	6.43 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NVIDIA Parabricks on 4 NVIDIA A100 GPUs (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12843', column 'A100' (PDF page text)
Configuration: NVIDIA Parabricks on 4 NVIDIA A100 GPUs (UiO HPC) (Samarakoon et al. 2025)	Protocol: WGS germline pipeline wall-clock, HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025 Table S3b.1) Dataset: Ten WGS samples: six Illumina Platinum pedigree high-coverage and four 1000 Genomes phase 3 low-coverage	17.6 runtime minute · lower Uncertainty: Not reported by the source: Single recorded run per cell; no repeats or intervals printed Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source NVIDIA Parabricks on 4 NVIDIA A100 GPUs (UiO HPC), HaplotypeCaller or DRAGEN GSVC calling stage (Samarakoon et al. 2025) model-execution-20261009-protocol-samarakoon2025-hc Aggregation: Not reported Benchmarking accelerated next-generation sequencing analysis pipelines; Samarakoon et al. 2025, supplementary materials (Tables S1-S4, supplementary texts) · Supplementary Table S3 'b.1) Variant calling via HC or DRAGEN GSVC', row 'NA12877', column 'A100' (PDF page text)