use-case-diagnostic-genomics-model-execution: attributes.setting
Setting of Select an execution workflow for large-scale diagnostic genomics
Published execution benchmarks, each on stated inputs: CPU-only GATK, Parabricks on L4, A100 and H100 GPUs and DRAGEN v4.2 on ten germline WGS samples (Samarakoon et al. 2025); two germline and four somatic callers on CPU and 2, 4 and 8 GPU cloud and DGX machines on one HG002 30x genome (O'Connell et al. 2023); Sentieon DNASeq and Parabricks Germline on Google Cloud machines of similar hourly cost, five exomes and five genomes (Franzoso et al. 2025); the DRAGEN 4.2 developer total runtime for HG002, 1,838.5 seconds on one hardware configuration and 5,521.21 seconds on an AWS f1.4xlarge configuration, whose stage times cannot be summed because of concurrency; Parabricks v4.3.0 on V100 and A100 nodes against the CPU GATK equivalent at five read depths of human WGS (Marangoni et al. 2026); three Sentieon DNAscope pipelines on one Azure instance (Hu et al. 2026); GenomeOcean inference in BF16 and FP8 on one H100 with microbial genomes (Yu et al. 2026); and LoRA fine-tuning and test-set scoring time of Nucleotide Transformer 500M on 2 × TITAN Xp, and fine-tuning time of pruned DNABERT-2 on 2 × Quadro RTX 8000, on a human eQTL variant classification task (Hegde et al. 2025). Four further linked studies are withheld pending source concerns: Clair3 and DeepVariant on HG003 long reads (Zheng et al. 2026), DNA language model inference on one A100 (Aspidova et al. 2026), Evo 2 embedding extraction for all ClinVar variants (Pearce et al. 2026) and Nucleotide Transformer IA3 fine-tuning time (Dalla-Torre et al. 2025). Pretraining compute for NTv3 and HyenaDNA is linked as outside scope. Hardware differs within most comparisons, so differences mix software and hardware.
Updated for the Hegde et al. 2025 judgements that became active in PR #169, which make a second linked foundation-model study, and for the newly linked withheld and outside-scope studies. Historical releases retain the previous value.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
7 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field attributes.setting Context-only references | Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction Store: reviewed judgements use-case-mapping-gfm-guide-20261014-hegde2025-eqtl-5-epochs and -eqtl-convergence become active; the EVEE and Nucleotide Transformer IA3 judgements are reviewed and withheld; the NTv3 and HyenaDNA judgements are outside scope Version: Genes 16(11):1358, 2025; PMC12652071 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Previous value Published execution benchmarks, each on stated inputs: CPU-only GATK, Parabricks on L4, A100 and H100 GPUs and DRAGEN v4.2 on ten germline WGS samples (Samarakoon et al. 2025); two germline and four somatic callers on CPU and 2, 4 and 8 GPU cloud and DGX machines on one HG002 30x genome (O'Connell et al. 2023); Sentieon DNASeq and Parabricks Germline on Google Cloud machines of similar hourly cost, five exomes and five genomes (Franzoso et al. 2025); the DRAGEN 4.2 developer total runtime for HG002, 1,838.5 seconds on one hardware configuration and 5,521.21 seconds on an AWS f1.4xlarge configuration, whose stage times cannot be summed because of concurrency; Parabricks v4.3.0 on V100 and A100 nodes against the CPU GATK equivalent at five read depths of human WGS (Marangoni et al. 2026); three Sentieon DNAscope pipelines on one Azure instance (Hu et al. 2026); and GenomeOcean inference in BF16 and FP8 on one H100 with microbial genomes (Yu et al. 2026). Two further linked studies, Clair3 and DeepVariant on HG003 long reads (Zheng et al. 2026) and DNA language model inference on one A100 (Aspidova et al. 2026), are withheld pending source concerns. Hardware differs within most comparisons, so differences mix software and hardware. Context-only references | Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction Store: reviewed judgements use-case-mapping-gfm-guide-20261014-hegde2025-eqtl-5-epochs and -eqtl-convergence become active; the EVEE and Nucleotide Transformer IA3 judgements are reviewed and withheld; the NTv3 and HyenaDNA judgements are outside scope Version: Genes 16(11):1358, 2025; PMC12652071 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Source location Store: reviewed judgements use-case-mapping-gfm-guide-20261014-hegde2025-eqtl-5-epochs and -eqtl-convergence become active; the EVEE and Nucleotide Transformer IA3 judgements are reviewed and withheld; the NTv3 and HyenaDNA judgements are outside scope Context-only references | Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction Store: reviewed judgements use-case-mapping-gfm-guide-20261014-hegde2025-eqtl-5-epochs and -eqtl-convergence become active; the EVEE and Nucleotide Transformer IA3 judgements are reviewed and withheld; the NTv3 and HyenaDNA judgements are outside scope Version: Genes 16(11):1358, 2025; PMC12652071 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed value Published execution benchmarks, each on stated inputs: CPU-only GATK, Parabricks on L4, A100 and H100 GPUs and DRAGEN v4.2 on ten germline WGS samples (Samarakoon et al. 2025); two germline and four somatic callers on CPU and 2, 4 and 8 GPU cloud and DGX machines on one HG002 30x genome (O'Connell et al. 2023); Sentieon DNASeq and Parabricks Germline on Google Cloud machines of similar hourly cost, five exomes and five genomes (Franzoso et al. 2025); the DRAGEN 4.2 developer total runtime for HG002, 1,838.5 seconds on one hardware configuration and 5,521.21 seconds on an AWS f1.4xlarge configuration, whose stage times cannot be summed because of concurrency; Parabricks v4.3.0 on V100 and A100 nodes against the CPU GATK equivalent at five read depths of human WGS (Marangoni et al. 2026); three Sentieon DNAscope pipelines on one Azure instance (Hu et al. 2026); GenomeOcean inference in BF16 and FP8 on one H100 with microbial genomes (Yu et al. 2026); and LoRA fine-tuning and test-set scoring time of Nucleotide Transformer 500M on 2 × TITAN Xp, and fine-tuning time of pruned DNABERT-2 on 2 × Quadro RTX 8000, on a human eQTL variant classification task (Hegde et al. 2025). Four further linked studies are withheld pending source concerns: Clair3 and DeepVariant on HG003 long reads (Zheng et al. 2026), DNA language model inference on one A100 (Aspidova et al. 2026), Evo 2 embedding extraction for all ClinVar variants (Pearce et al. 2026) and Nucleotide Transformer IA3 fine-tuning time (Dalla-Torre et al. 2025). Pretraining compute for NTv3 and HyenaDNA is linked as outside scope. Hardware differs within most comparisons, so differences mix software and hardware. Context-only references | Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction Store: reviewed judgements use-case-mapping-gfm-guide-20261014-hegde2025-eqtl-5-epochs and -eqtl-convergence become active; the EVEE and Nucleotide Transformer IA3 judgements are reviewed and withheld; the NTv3 and HyenaDNA judgements are outside scope Version: Genes 16(11):1358, 2025; PMC12652071 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Description Updated for the Hegde et al. 2025 judgements that became active in PR #169, which make a second linked foundation-model study, and for the newly linked withheld and outside-scope studies. Historical releases retain the previous value. Context-only references | Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction Store: reviewed judgements use-case-mapping-gfm-guide-20261014-hegde2025-eqtl-5-epochs and -eqtl-convergence become active; the EVEE and Nucleotide Transformer IA3 judgements are reviewed and withheld; the NTv3 and HyenaDNA judgements are outside scope Version: Genes 16(11):1358, 2025; PMC12652071 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: subject use-case-diagnostic-genomics-model-execution Context-only references | Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction Store: reviewed judgements use-case-mapping-gfm-guide-20261014-hegde2025-eqtl-5-epochs and -eqtl-convergence become active; the EVEE and Nucleotide Transformer IA3 judgements are reviewed and withheld; the NTv3 and HyenaDNA judgements are outside scope Version: Genes 16(11):1358, 2025; PMC12652071 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Name use-case-diagnostic-genomics-model-execution: attributes.setting Context-only references | Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction Store: reviewed judgements use-case-mapping-gfm-guide-20261014-hegde2025-eqtl-5-epochs and -eqtl-convergence become active; the EVEE and Nucleotide Transformer IA3 judgements are reviewed and withheld; the NTv3 and HyenaDNA judgements are outside scope Version: Genes 16(11):1358, 2025; PMC12652071 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction · Original source · Genes 16(11):1358, 2025; PMC12652071 full-text XML
Technical metadata and extraction receipts
Stable ID: metadata-correction-gfm-guide-20261014-execution-setting
- field
- attributes.setting
- previous value
- Published execution benchmarks, each on stated inputs: CPU-only GATK, Parabricks on L4, A100 and H100 GPUs and DRAGEN v4.2 on ten germline WGS samples (Samarakoon et al. 2025); two germline and four somatic callers on CPU and 2, 4 and 8 GPU cloud and DGX machines on one HG002 30x genome (O'Connell et al. 2023); Sentieon DNASeq and Parabricks Germline on Google Cloud machines of similar hourly cost, five exomes and five genomes (Franzoso et al. 2025); the DRAGEN 4.2 developer total runtime for HG002, 1,838.5 seconds on one hardware configuration and 5,521.21 seconds on an AWS f1.4xlarge configuration, whose stage times cannot be summed because of concurrency; Parabricks v4.3.0 on V100 and A100 nodes against the CPU GATK equivalent at five read depths of human WGS (Marangoni et al. 2026); three Sentieon DNAscope pipelines on one Azure instance (Hu et al. 2026); and GenomeOcean inference in BF16 and FP8 on one H100 with microbial genomes (Yu et al. 2026). Two further linked studies, Clair3 and DeepVariant on HG003 long reads (Zheng et al. 2026) and DNA language model inference on one A100 (Aspidova et al. 2026), are withheld pending source concerns. Hardware differs within most comparisons, so differences mix software and hardware.
- value
- Published execution benchmarks, each on stated inputs: CPU-only GATK, Parabricks on L4, A100 and H100 GPUs and DRAGEN v4.2 on ten germline WGS samples (Samarakoon et al. 2025); two germline and four somatic callers on CPU and 2, 4 and 8 GPU cloud and DGX machines on one HG002 30x genome (O'Connell et al. 2023); Sentieon DNASeq and Parabricks Germline on Google Cloud machines of similar hourly cost, five exomes and five genomes (Franzoso et al. 2025); the DRAGEN 4.2 developer total runtime for HG002, 1,838.5 seconds on one hardware configuration and 5,521.21 seconds on an AWS f1.4xlarge configuration, whose stage times cannot be summed because of concurrency; Parabricks v4.3.0 on V100 and A100 nodes against the CPU GATK equivalent at five read depths of human WGS (Marangoni et al. 2026); three Sentieon DNAscope pipelines on one Azure instance (Hu et al. 2026); GenomeOcean inference in BF16 and FP8 on one H100 with microbial genomes (Yu et al. 2026); and LoRA fine-tuning and test-set scoring time of Nucleotide Transformer 500M on 2 × TITAN Xp, and fine-tuning time of pruned DNABERT-2 on 2 × Quadro RTX 8000, on a human eQTL variant classification task (Hegde et al. 2025). Four further linked studies are withheld pending source concerns: Clair3 and DeepVariant on HG003 long reads (Zheng et al. 2026), DNA language model inference on one A100 (Aspidova et al. 2026), Evo 2 embedding extraction for all ClinVar variants (Pearce et al. 2026) and Nucleotide Transformer IA3 fine-tuning time (Dalla-Torre et al. 2025). Pretraining compute for NTv3 and HyenaDNA is linked as outside scope. Hardware differs within most comparisons, so differences mix software and hardware.
- source locator
- Store: reviewed judgements use-case-mapping-gfm-guide-20261014-hegde2025-eqtl-5-epochs and -eqtl-convergence become active; the EVEE and Nucleotide Transformer IA3 judgements are reviewed and withheld; the NTv3 and HyenaDNA judgements are outside scope
- review
- method: source-hash-verification; scope-review; reviewer: claude; reviewer note: Claude (Opus 5.5) review agent review-169, independent of the agent that drafted these judgements for issue #162; no human review claimed; date: 2026-10-14; note: Applied by the independent reviewer of PR #169. See docs/reviews/use-cases/diagnostic-genomics-model-execution-judgements-2026-10-14.md.