Dataset

HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)

Evidence concern: excluded from comparisons

Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999

Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement

Deletion truth set used by Nardone et al.

Research readiness

These checks assess whether the evidence supports a reproducible investigation. A source-checked score alone does not meet these requirements.

Release 2026-10-09-9307685239b3 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

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artifact hashes: verification is missing
join integrity: verification is missing
score semantics: verification is missing
metric replay: verification is missing

Verified: Not verified

Evidence incomplete

Investigate discrepancies

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Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
artifact hashes: verification is missing
join integrity: verification is missing
score semantics: verification is missing
metric replay: verification is missing
annotations: verification is missing
dependence: verification is missing

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
artifact hashes: verification is missing
join integrity: verification is missing
score semantics: verification is missing
recipe pinned: verification is missing
resource estimate: verification is missing

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
artifact hashes: verification is missing
join integrity: verification is missing
score semantics: verification is missing
independent validation: verification is missing
overlap checked: verification is missing

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Read reviewed discrepancy investigations

Evaluation results

10 evaluations · 240 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	NA f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, I62; Method CNVnator; Interval 100-499; column F1Score
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.112 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, I64; Method CNVnator; Interval 1000-4999; column F1Score
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.832 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, I66; Method CNVnator; Interval 10000-19999; column F1Score
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	NA f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, I61; Method CNVnator; Interval 50-99; column F1Score
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	NA f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, I63; Method CNVnator; Interval 500-999; column F1Score
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.533 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, I65; Method CNVnator; Interval 5000-9999; column F1Score
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.0415 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, I68; Method CNVnator; Interval ALL; column F1Score
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.398 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, I67; Method CNVnator; Interval >20000; column F1Score
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	NA precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, G62; Method CNVnator; Interval 100-499; column Precision
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.952 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, G64; Method CNVnator; Interval 1000-4999; column Precision
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.783 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, G66; Method CNVnator; Interval 10000-19999; column Precision
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	NA precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, G61; Method CNVnator; Interval 50-99; column Precision
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	NA precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, G63; Method CNVnator; Interval 500-999; column Precision
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.868 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, G65; Method CNVnator; Interval 5000-9999; column Precision
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.688 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, G68; Method CNVnator; Interval ALL; column Precision
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.268 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, G67; Method CNVnator; Interval >20000; column Precision
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, H62; Method CNVnator; Interval 100-499; column Recall
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.0593 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, H64; Method CNVnator; Interval 1000-4999; column Recall
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.889 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, H66; Method CNVnator; Interval 10000-19999; column Recall
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, H61; Method CNVnator; Interval 50-99; column Recall
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, H63; Method CNVnator; Interval 500-999; column Recall
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.385 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, H65; Method CNVnator; Interval 5000-9999; column Recall
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.0214 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, H68; Method CNVnator; Interval ALL; column Recall
Configuration: CNVnator v0.4.1 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.769 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source CNVnator on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, H67; Method CNVnator; Interval >20000; column Recall
Configuration: DELLY v1.1.5 (Nardone et al.)	Protocol: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1) Dataset: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)	0.726 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Results 3.1 prose gives inGAP in the 5000-9999 bp bin as F1 97%, precision 92%, recall 94%. Table S1 rows for inGAP 5000-9999 print F1 0.9466, precision 0.9714, recall 0.9231. The prose values are not consistent with each other (F1 cannot exceed both precision and recall) or with the table. Table values are recorded; prose values are not.A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Results 3.1 paragraph 2 versus TableS1.xlsx Method inGAP, Interval 5000-9999 Short-read input depth and alignment for Table S1 are stated inconsistently: Methods 2.2 says the 65x reads were subsampled to 25x and aligned with bwa-mem2 for preliminary evaluations; Results 3.1 says the HG002 data were previously aligned using the DRAGEN pipeline; the Data Availability Statement cites 30x Illumina HG002 2x250 reads. Which depth and aligner produced Table S1 is not resolved, so these results should not be compared automatically with other HG002 tables.Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Methods 2.2 paragraph 1; Results 3.1 paragraph 1; Data Availability Statement Methods, coverage and source DELLY on HG002 deletions (Nardone et al.) cnv-20261009-protocol-nardone2025-hg002-del-wittyer Aggregation: Not reported A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies; Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · TableS1.xlsx, I22; Method DELLY; Interval 100-499; column F1Score

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12 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-09-9307685239b3
Property and statement	Original source and location	Review and provenance
attributes.population Public HG002 Illumina reads; depth and aligner for Table S1 stated inconsistently (see source evidence concern) Context-only references	A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies Original source ↗ Methods 2.1 and 2.2; Data Availability Statement Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Biomedicines 13(8):1949, published 2025-08-09; PMC12383524 full-text XML Retrieved: 2026-10-09T15:28:17Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.population` Source artifact SHA-256: `45317b1396f900fd8bcbe6e95519a4b475fda4c5ee416c63752811b71e154eb8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.population Public HG002 Illumina reads; depth and aligner for Table S1 stated inconsistently (see source evidence concern) Context-only references	Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) Original source ↗ Methods 2.1 and 2.2; Data Availability Statement Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: TableS1.xlsx inside biomedicines-13-01949-s001.zip Retrieved: 2026-10-09T15:28:17Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.population` Source artifact SHA-256: `1e84dde9132aa977c069e3ce50132247a83969316cbd7c98f238ac54db032b14` Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 86c46fdc3e9125ae8e025ac4d1c9129dd4631039abd56019581e242dc3ae3d70; biomedicines-13-01949-s001.zip 678880a4c36070dfaf0813421d82a4e2747a85cb5a85c8c886b321a58be8ecf9. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. Inspected artifact
attributes.source_locator Methods 2.1 and 2.2; Data Availability Statement Context-only references	A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies Original source ↗ Methods 2.1 and 2.2; Data Availability Statement Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Biomedicines 13(8):1949, published 2025-08-09; PMC12383524 full-text XML Retrieved: 2026-10-09T15:28:17Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.source_locator` Source artifact SHA-256: `45317b1396f900fd8bcbe6e95519a4b475fda4c5ee416c63752811b71e154eb8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.source_locator Methods 2.1 and 2.2; Data Availability Statement Context-only references	Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) Original source ↗ Methods 2.1 and 2.2; Data Availability Statement Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: TableS1.xlsx inside biomedicines-13-01949-s001.zip Retrieved: 2026-10-09T15:28:17Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.source_locator` Source artifact SHA-256: `1e84dde9132aa977c069e3ce50132247a83969316cbd7c98f238ac54db032b14` Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 86c46fdc3e9125ae8e025ac4d1c9129dd4631039abd56019581e242dc3ae3d70; biomedicines-13-01949-s001.zip 678880a4c36070dfaf0813421d82a4e2747a85cb5a85c8c886b321a58be8ecf9. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. Inspected artifact
attributes.split Single HG002 sample Context-only references	A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies Original source ↗ Methods 2.1 and 2.2; Data Availability Statement Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Biomedicines 13(8):1949, published 2025-08-09; PMC12383524 full-text XML Retrieved: 2026-10-09T15:28:17Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.split` Source artifact SHA-256: `45317b1396f900fd8bcbe6e95519a4b475fda4c5ee416c63752811b71e154eb8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.split Single HG002 sample Context-only references	Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) Original source ↗ Methods 2.1 and 2.2; Data Availability Statement Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: TableS1.xlsx inside biomedicines-13-01949-s001.zip Retrieved: 2026-10-09T15:28:17Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.split` Source artifact SHA-256: `1e84dde9132aa977c069e3ce50132247a83969316cbd7c98f238ac54db032b14` Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 86c46fdc3e9125ae8e025ac4d1c9129dd4631039abd56019581e242dc3ae3d70; biomedicines-13-01949-s001.zip 678880a4c36070dfaf0813421d82a4e2747a85cb5a85c8c886b321a58be8ecf9. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. Inspected artifact
attributes.version GIAB NIST_SV_v0.6 HG002 Tier 1 deletions (5,465 on hg19) lifted to hg38 with CrossMap 0.7.3, 5,414 retained Context-only references	A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies Original source ↗ Methods 2.1 and 2.2; Data Availability Statement Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Biomedicines 13(8):1949, published 2025-08-09; PMC12383524 full-text XML Retrieved: 2026-10-09T15:28:17Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.version` Source artifact SHA-256: `45317b1396f900fd8bcbe6e95519a4b475fda4c5ee416c63752811b71e154eb8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.version GIAB NIST_SV_v0.6 HG002 Tier 1 deletions (5,465 on hg19) lifted to hg38 with CrossMap 0.7.3, 5,414 retained Context-only references	Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) Original source ↗ Methods 2.1 and 2.2; Data Availability Statement Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: TableS1.xlsx inside biomedicines-13-01949-s001.zip Retrieved: 2026-10-09T15:28:17Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.version` Source artifact SHA-256: `1e84dde9132aa977c069e3ce50132247a83969316cbd7c98f238ac54db032b14` Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 86c46fdc3e9125ae8e025ac4d1c9129dd4631039abd56019581e242dc3ae3d70; biomedicines-13-01949-s001.zip 678880a4c36070dfaf0813421d82a4e2747a85cb5a85c8c886b321a58be8ecf9. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. Inspected artifact
description Deletion truth set used by Nardone et al. Context-only references	A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies Original source ↗ Methods 2.1 and 2.2; Data Availability Statement Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Biomedicines 13(8):1949, published 2025-08-09; PMC12383524 full-text XML Retrieved: 2026-10-09T15:28:17Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `description` Source artifact SHA-256: `45317b1396f900fd8bcbe6e95519a4b475fda4c5ee416c63752811b71e154eb8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
description Deletion truth set used by Nardone et al. Context-only references	Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) Original source ↗ Methods 2.1 and 2.2; Data Availability Statement Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: TableS1.xlsx inside biomedicines-13-01949-s001.zip Retrieved: 2026-10-09T15:28:17Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `description` Source artifact SHA-256: `1e84dde9132aa977c069e3ce50132247a83969316cbd7c98f238ac54db032b14` Hash scope: artifact_sha256 is the inner supplementary file. Containers: europepmc_supplementary_zip 86c46fdc3e9125ae8e025ac4d1c9129dd4631039abd56019581e242dc3ae3d70; biomedicines-13-01949-s001.zip 678880a4c36070dfaf0813421d82a4e2747a85cb5a85c8c886b321a58be8ecf9. The Europe PMC zip is rebuilt per request, so its hash describes one retrieval only. Inspected artifact

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Sources and history

Release 2026-10-09-9307685239b3 · Record review: source checked

2 source records and release history

A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies · Original source · Biomedicines 13(8):1949, published 2025-08-09; PMC12383524 full-text XML
Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) · Original source · TableS1.xlsx inside biomedicines-13-01949-s001.zip

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Technical metadata and extraction receipts

Stable ID: cnv-20261009-data-nardone2025-hg002-giab-sv06-tier1-del-hg38

areas: dna-genomes
contexts: clinical_research
version: GIAB NIST_SV_v0.6 HG002 Tier 1 deletions (5,465 on hg19) lifted to hg38 with CrossMap 0.7.3, 5,414 retained
split: Single HG002 sample
population: Public HG002 Illumina reads; depth and aligner for Table S1 stated inconsistently (see source evidence concern)
source locator: Methods 2.1 and 2.2; Data Availability Statement
missing metadata: population detail: reason: conflicting; note: 25x (Methods 2.2) versus 30x (Data Availability); unresolved. bwa-mem2 (Methods 2.2) versus DRAGEN pipeline (Results 3.1); unresolved.; scored count: reason: unreported; note: Methods 2.1 gives 5,414 deletions after liftover; Table S1 TP+FN is 4,159 for every caller. Why 1,255 deletions are not scored is not stated.

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