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-scorefraction · 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-scorefraction · 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-scorefraction · 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-scorefraction · 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-scorefraction · 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-scorefraction · 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-scorefraction · 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-scorefraction · 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 precisionfraction · 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 precisionfraction · 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 precisionfraction · 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 precisionfraction · 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 precisionfraction · 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 precisionfraction · 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 precisionfraction · 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 precisionfraction · 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 recallfraction · 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 recallfraction · 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 recallfraction · 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 recallfraction · 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 recallfraction · 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 recallfraction · 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 recallfraction · 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 recallfraction · 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