Configuration

CPU tools on AWS c6i.8xlarge (O'Connell et al. 2023)

CPU tools on AWS c6i.8xlarge as run in Table 1.

Overview

CPU tools on AWS c6i.8xlarge 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-aws-c6i-8xlarge

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
foundation model eligible: false
reported name: CPU tools on AWS c6i.8xlarge
hardware: description: AWS c6i.8xlarge: Intel Xeon Ice Lake 8375C, 32 vCPUs, 64 GiB RAM, 800 GB EBS
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 AWS c6i.8xlarge (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	29.9 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-deepvariant Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 1 (AWS, C6i.8xlarge, DeepVariant), column 'Cost ($)'
Configuration: CPU tools on AWS c6i.8xlarge (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	1320 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-deepvariant Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 1 (AWS, C6i.8xlarge, DeepVariant), column 'Time (min)'
Configuration: CPU tools on AWS c6i.8xlarge (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	22 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-deepvariant Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 1 (AWS, C6i.8xlarge, DeepVariant), column 'Time (h)'
Configuration: CPU tools on AWS c6i.8xlarge (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	49.3 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-haplotypecaller Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 12 (AWS, C6i.8xlarge, HaplotypeCaller), column 'Cost ($)'
Configuration: CPU tools on AWS c6i.8xlarge (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	2180 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-haplotypecaller Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 12 (AWS, C6i.8xlarge, HaplotypeCaller), column 'Time (min)'
Configuration: CPU tools on AWS c6i.8xlarge (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	36.3 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-haplotypecaller Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 12 (AWS, C6i.8xlarge, HaplotypeCaller), column 'Time (h)'
Configuration: CPU tools on AWS c6i.8xlarge (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	4.1 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-lofreq Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 23 (AWS, C6i.8xlarge, LoFreq), column 'Cost ($)'
Configuration: CPU tools on AWS c6i.8xlarge (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	180 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-lofreq Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 23 (AWS, C6i.8xlarge, LoFreq), column 'Time (min)'
Configuration: CPU tools on AWS c6i.8xlarge (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	3 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-lofreq Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 23 (AWS, C6i.8xlarge, LoFreq), column 'Time (h)'
Configuration: CPU tools on AWS c6i.8xlarge (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	9.6 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-muse Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 34 (AWS, C6i.8xlarge, Muse), column 'Cost ($)'
Configuration: CPU tools on AWS c6i.8xlarge (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	425 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-muse Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 34 (AWS, C6i.8xlarge, Muse), column 'Time (min)'
Configuration: CPU tools on AWS c6i.8xlarge (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	7.09 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-muse Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 34 (AWS, C6i.8xlarge, Muse), column 'Time (h)'
Configuration: CPU tools on AWS c6i.8xlarge (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	9.4 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-mutect2 Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 45 (AWS, C6i.8xlarge, Mutect2), column 'Cost ($)'
Configuration: CPU tools on AWS c6i.8xlarge (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	415 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-mutect2 Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 45 (AWS, C6i.8xlarge, Mutect2), column 'Time (min)'
Configuration: CPU tools on AWS c6i.8xlarge (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	6.91 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-mutect2 Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 45 (AWS, C6i.8xlarge, Mutect2), column 'Time (h)'
Configuration: CPU tools on AWS c6i.8xlarge (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	8.88 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-somaticsniper Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 56 (AWS, C6i.8xlarge, SomaticSniper), column 'Cost ($)'
Configuration: CPU tools on AWS c6i.8xlarge (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	392 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-somaticsniper Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 56 (AWS, C6i.8xlarge, SomaticSniper), column 'Time (min)'
Configuration: CPU tools on AWS c6i.8xlarge (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	6.53 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 AWS c6i.8xlarge (O'Connell et al. 2023) model-execution-20261009-protocol-oconnell2023-somaticsniper Aggregation: Not reported Accelerating genomic workflows using NVIDIA Parabricks · Table 1, row 56 (AWS, C6i.8xlarge, SomaticSniper), column 'Time (h)'