Configuration

CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)

CPU tools on GCP n2-standard-32 as run in Table 1.

Overview

CPU tools on GCP n2-standard-32 as run in Table 1.

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Accelerating genomic workflows using NVIDIA Parabricks · Original source · BMC Bioinformatics 24:221, published 2023-05-31; PMC10230726 full-text XML

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Technical metadata and extraction receipts

Stable ID: model-execution-20261009-config-oconnell2023-gcp-n2-standard-32

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
foundation model eligible: false
reported name: CPU tools on GCP n2-standard-32
hardware: description: GCP n2-standard-32: Intel Xeon Cascade Lake, 32 vCPUs, 128 GB RAM
source locator: Table 1 VM-type column; Methods 'GCP configuration', 'AWS configuration', 'DGX configuration'
protocol: Snakemake v6.6.1 CPU workflows matching the Parabricks steps: bwa mem 0.7.15, Samtools, GATK 4.2.0.0 and HaplotypeCaller 4.2.0.0 or DeepVariant 1.1.0; Mutect2 4.2.0.0, SomaticSniper 1.0.5.0, LoFreq 2.1, MuSE 2.0 (single thread)
version: HaplotypeCaller 4.2.0.0; DeepVariant 1.1.0; Mutect2 4.2.0.0; SomaticSniper 1.0.5.0; LoFreq 2.1; MuSE 2.0

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: DeepVariant execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: HG002 (GIAB) WGS FASTQ down-sampled to 30x, precisionFDA Truth Challenge V2	32.9 compute-cost us-dollar · 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 DeepVariant on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-deepvariant Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 5 (GCP, n2-32, DeepVariant), column 'Cost ($)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: DeepVariant execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: HG002 (GIAB) WGS FASTQ down-sampled to 30x, precisionFDA Truth Challenge V2	1130 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 DeepVariant on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-deepvariant Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 5 (GCP, n2-32, DeepVariant), column 'Time (min)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: DeepVariant execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: HG002 (GIAB) WGS FASTQ down-sampled to 30x, precisionFDA Truth Challenge V2	18.8 runtime hour · 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 DeepVariant on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-deepvariant Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 5 (GCP, n2-32, DeepVariant), column 'Time (h)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: HaplotypeCaller execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: HG002 (GIAB) WGS FASTQ down-sampled to 30x, precisionFDA Truth Challenge V2	67.9 compute-cost us-dollar · 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 HaplotypeCaller on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-haplotypecaller Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 16 (GCP, n2-32, HaplotypeCaller), column 'Cost ($)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: HaplotypeCaller execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: HG002 (GIAB) WGS FASTQ down-sampled to 30x, precisionFDA Truth Challenge V2	2330 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 HaplotypeCaller on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-haplotypecaller Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 16 (GCP, n2-32, HaplotypeCaller), column 'Time (min)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: HaplotypeCaller execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: HG002 (GIAB) WGS FASTQ down-sampled to 30x, precisionFDA Truth Challenge V2	38.8 runtime hour · 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 HaplotypeCaller on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-haplotypecaller Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 16 (GCP, n2-32, HaplotypeCaller), column 'Time (h)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: LoFreq execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: Synthetic tumour BAM: HG002 30x with 198 SNVs added by SomatoSim v1.0.0	8.1 compute-cost us-dollar · 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 LoFreq on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-lofreq Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 27 (GCP, N2-32, LoFreq), column 'Cost ($)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: LoFreq execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: Synthetic tumour BAM: HG002 30x with 198 SNVs added by SomatoSim v1.0.0	278 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 LoFreq on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-lofreq Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 27 (GCP, N2-32, LoFreq), column 'Time (min)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: LoFreq execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: Synthetic tumour BAM: HG002 30x with 198 SNVs added by SomatoSim v1.0.0	4.63 runtime hour · 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 LoFreq on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-lofreq Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 27 (GCP, N2-32, LoFreq), column 'Time (h)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: Muse execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: Synthetic tumour BAM: HG002 30x with 198 SNVs added by SomatoSim v1.0.0	18.1 compute-cost us-dollar · 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 Muse on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-muse Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 38 (GCP, N2_32, Muse), column 'Cost ($)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: Muse execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: Synthetic tumour BAM: HG002 30x with 198 SNVs added by SomatoSim v1.0.0	622 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 Muse on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-muse Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 38 (GCP, N2_32, Muse), column 'Time (min)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: Muse execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: Synthetic tumour BAM: HG002 30x with 198 SNVs added by SomatoSim v1.0.0	10.4 runtime hour · 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 Muse on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-muse Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 38 (GCP, N2_32, Muse), column 'Time (h)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: Mutect2 execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: Synthetic tumour BAM: HG002 30x with 198 SNVs added by SomatoSim v1.0.0	14.2 compute-cost us-dollar · 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 Mutect2 on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-mutect2 Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 49 (GCP, N2_32, Mutect2), column 'Cost ($)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: Mutect2 execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: Synthetic tumour BAM: HG002 30x with 198 SNVs added by SomatoSim v1.0.0	488 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 Mutect2 on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-mutect2 Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 49 (GCP, N2_32, Mutect2), column 'Time (min)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: Mutect2 execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: Synthetic tumour BAM: HG002 30x with 198 SNVs added by SomatoSim v1.0.0	8.13 runtime hour · 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 Mutect2 on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-mutect2 Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 49 (GCP, N2_32, Mutect2), column 'Time (h)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: SomaticSniper execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: Synthetic tumour BAM: HG002 30x with 198 SNVs added by SomatoSim v1.0.0	14.1 compute-cost us-dollar · 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 SomaticSniper on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-somaticsniper Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 60 (GCP, N2_32, SomaticSniper), column 'Cost ($)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: SomaticSniper execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: Synthetic tumour BAM: HG002 30x with 198 SNVs added by SomatoSim v1.0.0	483 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 SomaticSniper on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-somaticsniper Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 60 (GCP, N2_32, SomaticSniper), column 'Time (min)'
Configuration: CPU tools on GCP n2-standard-32 (O'Connell et al. 2023)	Protocol: SomaticSniper execution on CPU and GPU cloud and DGX machines (O'Connell et al. 2023 Table 1) Dataset: Synthetic tumour BAM: HG002 30x with 198 SNVs added by SomatoSim v1.0.0	8.05 runtime hour · 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 SomaticSniper on CPU tools on GCP n2-standard-32 (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-somaticsniper Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 60 (GCP, N2_32, SomaticSniper), column 'Time (h)'