Evaluation

inGAP on HG002 deletions (Nardone et al.)

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

Published CNV caller comparison; transcribed, not reproduced.

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Release 2026-10-09-8eac2440869c · Evidence verified: Not verified

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Read reviewed discrepancy investigations

Evaluation results

1 evaluation · 24 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: inGAP v1.6.0 (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)	0.326 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 inGAP 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, I14; Method inGAP; Interval 100-499; column F1Score
Configuration: inGAP v1.6.0 (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)	0.93 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 inGAP 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, I16; Method inGAP; Interval 1000-4999; column F1Score
Configuration: inGAP v1.6.0 (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)	0.869 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 inGAP 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, I18; Method inGAP; Interval 10000-19999; column F1Score
Configuration: inGAP v1.6.0 (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 inGAP 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, I13; Method inGAP; Interval 50-99; column F1Score
Configuration: inGAP v1.6.0 (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)	0.458 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 inGAP 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, I15; Method inGAP; Interval 500-999; column F1Score
Configuration: inGAP v1.6.0 (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)	0.947 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 inGAP 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, I17; Method inGAP; Interval 5000-9999; column F1Score
Configuration: inGAP v1.6.0 (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)	0.362 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 inGAP 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, I20; Method inGAP; Interval ALL; column F1Score
Configuration: inGAP v1.6.0 (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)	0.682 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 inGAP 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, I19; Method inGAP; Interval >20000; column F1Score
Configuration: inGAP v1.6.0 (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)	0.669 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 inGAP 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, G14; Method inGAP; Interval 100-499; column Precision
Configuration: inGAP v1.6.0 (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)	0.978 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 inGAP 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, G16; Method inGAP; Interval 1000-4999; column Precision
Configuration: inGAP v1.6.0 (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)	0.85 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 inGAP 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, G18; Method inGAP; Interval 10000-19999; column Precision
Configuration: inGAP v1.6.0 (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 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 inGAP 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, G13; Method inGAP; Interval 50-99; column Precision
Configuration: inGAP v1.6.0 (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)	0.324 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 inGAP 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, G15; Method inGAP; Interval 500-999; column Precision
Configuration: inGAP v1.6.0 (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)	0.971 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 inGAP 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, G17; Method inGAP; Interval 5000-9999; column Precision
Configuration: inGAP v1.6.0 (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)	0.635 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 inGAP 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, G20; Method inGAP; Interval ALL; column Precision
Configuration: inGAP v1.6.0 (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)	0.571 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 inGAP 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, G19; Method inGAP; Interval >20000; column Precision
Configuration: inGAP v1.6.0 (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)	0.215 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 inGAP 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, H14; Method inGAP; Interval 100-499; column Recall
Configuration: inGAP v1.6.0 (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)	0.887 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 inGAP 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, H16; Method inGAP; Interval 1000-4999; column Recall
Configuration: inGAP v1.6.0 (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 inGAP 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, H18; Method inGAP; Interval 10000-19999; column Recall
Configuration: inGAP v1.6.0 (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 inGAP 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, H13; Method inGAP; Interval 50-99; column Recall
Configuration: inGAP v1.6.0 (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)	0.782 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 inGAP 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, H15; Method inGAP; Interval 500-999; column Recall
Configuration: inGAP v1.6.0 (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)	0.923 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 inGAP 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, H17; Method inGAP; Interval 5000-9999; column Recall
Configuration: inGAP v1.6.0 (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)	0.253 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 inGAP 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, H20; Method inGAP; Interval ALL; column Recall
Configuration: inGAP v1.6.0 (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)	0.846 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 inGAP 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, H19; Method inGAP; Interval >20000; column Recall

Source checking is not independent reproduction. Release 2026-10-09-8eac2440869c.

Evaluation procedure

cnv-20261009-protocol-nardone2025-hg002-del-wittyer

Configuration: inGAP v1.6.0 (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)

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-09
protocol id: cnv-20261009-protocol-nardone2025-hg002-del-wittyer
dataset version: GIAB SV v0.6 Tier 1 deletions lifted to hg38
split: Single HG002 sample
population: 5,414 benchmark deletions per Methods 2.1; Table S1 TP+FN is 4,159 for every caller and bin sums match the ALL row, so 4,159 deletions were scored. The article does not explain the difference.
inputs: Not reported
adaptation: Not reported
metric implementation: Witty.er v0.5.2 (Methods 2.4); matching parameters unreported
aggregation: Single sample, per length bin
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Single HG002 sample
Adaptation: Not reported
Scoring implementation: Witty.er v0.5.2 (Methods 2.4); matching parameters unreported

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

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.

36 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-09-8eac2440869c
Property and statement	Original source and location	Review and provenance
attributes.comparison.adaptation Not reported Context-only references	A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies Original source ↗ TableS1.xlsx rows 13-20 (Method inGAP) 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	missing or unspecified No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `45317b1396f900fd8bcbe6e95519a4b475fda4c5ee416c63752811b71e154eb8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.adaptation Not reported Context-only references	Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) Original source ↗ TableS1.xlsx rows 13-20 (Method inGAP) 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	missing or unspecified No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.adaptation` 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.comparison.aggregation Single sample, per length bin Context-only references	A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies Original source ↗ TableS1.xlsx rows 13-20 (Method inGAP) 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 independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `45317b1396f900fd8bcbe6e95519a4b475fda4c5ee416c63752811b71e154eb8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation Single sample, per length bin Context-only references	Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) Original source ↗ TableS1.xlsx rows 13-20 (Method inGAP) 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 independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.aggregation` 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.comparison.budget Not reported Context-only references	A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies Original source ↗ TableS1.xlsx rows 13-20 (Method inGAP) 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	missing or unspecified No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `45317b1396f900fd8bcbe6e95519a4b475fda4c5ee416c63752811b71e154eb8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget Not reported Context-only references	Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) Original source ↗ TableS1.xlsx rows 13-20 (Method inGAP) 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	missing or unspecified No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.budget` 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.comparison.dataset_version GIAB SV v0.6 Tier 1 deletions lifted to hg38 Context-only references	A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies Original source ↗ TableS1.xlsx rows 13-20 (Method inGAP) 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 independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `45317b1396f900fd8bcbe6e95519a4b475fda4c5ee416c63752811b71e154eb8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version GIAB SV v0.6 Tier 1 deletions lifted to hg38 Context-only references	Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) Original source ↗ TableS1.xlsx rows 13-20 (Method inGAP) 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 independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.dataset_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
attributes.comparison.inputs Not reported Context-only references	A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies Original source ↗ TableS1.xlsx rows 13-20 (Method inGAP) 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	missing or unspecified No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `45317b1396f900fd8bcbe6e95519a4b475fda4c5ee416c63752811b71e154eb8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs Not reported Context-only references	Nardone et al. 2025, Table S1 (ten short-read SV callers on HG002) Original source ↗ TableS1.xlsx rows 13-20 (Method inGAP) 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	missing or unspecified No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.inputs` 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 2026-10-09-8eac2440869c · 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-eval-nardone2025-ingap

areas: dna-genomes
contexts: clinical_research
origin: independent_paper
protocol: cnv-20261009-protocol-nardone2025-hg002-del-wittyer
version: Primary source as retrieved 2026-10-09
comparison: protocol id: cnv-20261009-protocol-nardone2025-hg002-del-wittyer; dataset version: GIAB SV v0.6 Tier 1 deletions lifted to hg38; split: Single HG002 sample; population: 5,414 benchmark deletions per Methods 2.1; Table S1 TP+FN is 4,159 for every caller and bin sums match the ALL row, so 4,159 deletions were scored. The article does not explain the difference.; inputs: Not reported; adaptation: Not reported; metric implementation: Witty.er v0.5.2 (Methods 2.4); matching parameters unreported; aggregation: Single sample, per length bin; budget: Not reported
source locator: TableS1.xlsx rows 13-20 (Method inGAP)
missing metadata: comparison.inputs: reason: conflicting; note: Depth and aligner conflict; see source evidence concern

Related records

system: inGAP v1.6.0 (Nardone et al.)
assessment: HG002 short-read deletion calling by length bin, witty.er (Nardone et al. Table S1)
data: HG002 GIAB SV v0.6 Tier 1 deletions lifted to GRCh38 (5,414)
evaluation: nardone2025-ingap f1-score (deletions, 100-499 bp)
evaluation: nardone2025-ingap f1-score (deletions, 1000-4999 bp)
evaluation: nardone2025-ingap f1-score (deletions, 10000-19999 bp)
evaluation: nardone2025-ingap f1-score (deletions, 50-99 bp)
evaluation: nardone2025-ingap f1-score (deletions, 500-999 bp)
evaluation: nardone2025-ingap f1-score (deletions, 5000-9999 bp)
evaluation: nardone2025-ingap f1-score (deletions, all sizes)
evaluation: nardone2025-ingap f1-score (deletions, over 20000 bp)
evaluation: nardone2025-ingap precision (deletions, 100-499 bp)
evaluation: nardone2025-ingap precision (deletions, 1000-4999 bp)
evaluation: nardone2025-ingap precision (deletions, 10000-19999 bp)
evaluation: nardone2025-ingap precision (deletions, 50-99 bp)
evaluation: nardone2025-ingap precision (deletions, 500-999 bp)
evaluation: nardone2025-ingap precision (deletions, 5000-9999 bp)
evaluation: nardone2025-ingap precision (deletions, all sizes)
evaluation: nardone2025-ingap precision (deletions, over 20000 bp)
evaluation: nardone2025-ingap recall (deletions, 100-499 bp)
evaluation: nardone2025-ingap recall (deletions, 1000-4999 bp)
evaluation: nardone2025-ingap recall (deletions, 10000-19999 bp)
evaluation: nardone2025-ingap recall (deletions, 50-99 bp)
evaluation: nardone2025-ingap recall (deletions, 500-999 bp)
evaluation: nardone2025-ingap recall (deletions, 5000-9999 bp)
evaluation: nardone2025-ingap recall (deletions, all sizes)
evaluation: nardone2025-ingap recall (deletions, over 20000 bp)

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