Contested result

DeepSomatic and Majority-vote consensus of somatic callers: A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing reverses the order

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Not yet reviewed
Ordering reversal
Different tasks across studies

A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing ranks DeepSomatic above Majority-vote consensus of somatic callers in 8 of 10 comparisons; other studies rank Majority-vote consensus of somatic callers above DeepSomatic in 20 of 20.

An automatic lead, not a finding of error. The results below are shown as published, everywhere on the site, until a reviewer decides otherwise.

Which studies agree

Prospectively frozen external… ranks Majority-vote consensus of somatic callers above DeepSomatic in all 20 comparisons that are not ties (4 are ties). A benchmarking study of individual… ranks DeepSomatic above Majority-vote consensus of somatic callers in 8 of its 12 comparisons and Majority-vote consensus of somatic callers higher in 2; 2 are ties.

Rank Majority-vote consensus of somatic callers higher (1): Prospectively frozen external…
Rank DeepSomatic higher (1): A benchmarking study of individual… (disagrees)
Mixed (0): none

Each paper sits where at least two thirds of its comparisons point; Mixed means neither model reaches two thirds. The larger, outlined dot is the paper that disagrees.

Majority-vote consensus of somatic callers higherTieDeepSomatic higherNumbers are counts of comparisons; the outlined bar is the paper that disagrees.

Papers compared (2)
Paper	Role	Ranks Majority-vote consensus of somatic callers higher	Ranks DeepSomatic higher	Ties
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing and 1 more record · DOI	Disagrees	2	8	2
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling and 1 more record · DOI	Agrees	20	0	4

Comparisons in A benchmarking study of individual… (12)

Protocol	Dataset	Metric	Majority-vote consensus of somatic callers	DeepSomatic	Higher
SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	F1 (indel only), fraction	0.752	0.812	DeepSomatic
SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	False positives (indel only), count	9	10	Majority-vote consensus of somatic callers
SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	False positive rate (indel only), fraction	5.98e-8	6.64e-8	Majority-vote consensus of somatic callers
SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	Precision (indel only), fraction	0.795	0.804	DeepSomatic
SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	Recall (indel only), fraction	0.76	0.82	DeepSomatic
SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	True positives (indel only), count	38	41	DeepSomatic
SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7)	SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	F1 (SNV only), fraction	0.881	0.901	DeepSomatic
SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7)	SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	False positives (SNV only), count	58	34	DeepSomatic
SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7)	SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	False positive rate (SNV only), fraction	3.85e-7	2.26e-7	DeepSomatic
SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7)	SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	Precision (SNV only), fraction	0.943	0.966	DeepSomatic
SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7)	SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	Recall (SNV only), fraction	0.838	0.843	Tie
SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7)	SEQC2 HCC1395/HCC1395BL WES, Fudan replicate (WES_FD_T_1), high-confidence regions	True positives (SNV only), count	972	978	Tie

Comparisons in Prospectively frozen external… (24)

Protocol	Dataset	Metric	Majority-vote consensus of somatic callers	DeepSomatic	Higher
HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	F1 (SNVs and indels, HG008 all-benchmark region), fraction	0.794	0.776	Majority-vote consensus of somatic callers
HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	False negatives (SNVs and indels, HG008 all-benchmark region), count	4710	6590	Majority-vote consensus of somatic callers
HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	False positives (SNVs and indels, HG008 all-benchmark region), count	7	133	Majority-vote consensus of somatic callers
HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	Precision (SNVs and indels, HG008 all-benchmark region), fraction	0.999	0.989	Majority-vote consensus of somatic callers
HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	Recall (SNVs and indels, HG008 all-benchmark region), fraction	0.741	0.638	Majority-vote consensus of somatic callers
HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	True positives (SNVs and indels, HG008 all-benchmark region), count	13500	11600	Majority-vote consensus of somatic callers
HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	F1 (indel only, HG008 primary region), fraction	0.809	0.69	Majority-vote consensus of somatic callers
HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	False negatives (indel only, HG008 primary region), count	1080	2320	Majority-vote consensus of somatic callers
HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	False positives (indel only, HG008 primary region), count	2	28	Majority-vote consensus of somatic callers
HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	Precision (indel only, HG008 primary region), fraction	0.999	0.989	Tie
HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	Recall (indel only, HG008 primary region), fraction	0.781	0.529	Majority-vote consensus of somatic callers
HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	True positives (indel only, HG008 primary region), count	3860	2610	Majority-vote consensus of somatic callers
HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	F1 (SNVs and indels, HG008 primary region), fraction	0.914	0.897	Majority-vote consensus of somatic callers
HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	False negatives (SNVs and indels, HG008 primary region), count	1190	2510	Majority-vote consensus of somatic callers
HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	False positives (SNVs and indels, HG008 primary region), count	5	124	Majority-vote consensus of somatic callers
HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	Precision (SNVs and indels, HG008 primary region), fraction	1	0.989	Majority-vote consensus of somatic callers
HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	Recall (SNVs and indels, HG008 primary region), fraction	0.915	0.821	Majority-vote consensus of somatic callers
HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	True positives (SNVs and indels, HG008 primary region), count	12800	11500	Majority-vote consensus of somatic callers
HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV')	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	F1 (SNV only, HG008 primary region), fraction	0.985	0.984	Tie
HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV')	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	False negatives (SNV only, HG008 primary region), count	113	186	Majority-vote consensus of somatic callers
HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV')	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	False positives (SNV only, HG008 primary region), count	3	96	Majority-vote consensus of somatic callers
HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV')	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	Precision (SNV only, HG008 primary region), fraction	1	0.989	Majority-vote consensus of somatic callers
HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV')	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	Recall (SNV only, HG008 primary region), fraction	0.988	0.98	Tie
HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV')	NIST/GIAB HG008 tumour-normal WGS (HG008-T pancreatic cancer cell line, matched normal), HG008-T draft somatic small-variant benchmark v0.3	True positives (SNV only, HG008 primary region), count	8970	8890	Tie

What disagrees

Other studies: rank Majority-vote consensus of somatic callers above DeepSomatic in 20 of 20 comparisons
This study: ranks DeepSomatic above Majority-vote consensus of somatic callers in 8 of 10 comparisons

Compared: DeepSomatic, Majority-vote consensus of somatic callers
Study that disagrees: A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing, Guille et al. 2025, Supplementary Table S7 (validation dataset)
Other studies: Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling, AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)
Rule: Ordering reversal; different tasks across studies
Model identity: Matched across studies partly through links not yet reviewed

The compared numbers

Each value links to its result record and source. Compare values within one protocol; the rule compares rankings, not raw values across protocols.

In the study that disagrees (20)
Study	Tool	Protocol or benchmark	Metric	Value
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	DeepSomatic-WES 1.7.0 (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	F1 (indel only)	0.812
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	DeepSomatic-WES 1.7.0 (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	False positives (indel only)	10
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	DeepSomatic-WES 1.7.0 (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	False positive rate (indel only)	6.64e-8
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	DeepSomatic-WES 1.7.0 (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	Precision (indel only)	0.804
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	DeepSomatic-WES 1.7.0 (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	Recall (indel only)	0.82
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	DeepSomatic-WES 1.7.0 (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	True positives (indel only)	41
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	DeepSomatic-WES 1.7.0 (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7)	F1 (SNV only)	0.901
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	DeepSomatic-WES 1.7.0 (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7)	False positives (SNV only)	34
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	DeepSomatic-WES 1.7.0 (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7)	False positive rate (SNV only)	2.26e-7
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	DeepSomatic-WES 1.7.0 (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7)	Precision (SNV only)	0.966
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	Vote ensemble Mutect2, Strelka, Varscan2, at least 2 agree (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	False positives (indel only)	9
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	Vote ensemble Mutect2, Strelka, Varscan2, at least 2 agree (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	False positive rate (indel only)	5.98e-8
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	Vote ensemble Mutect2, Strelka, Varscan2, at least 2 agree (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	Precision (indel only)	0.795
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	Vote ensemble Mutect2, Strelka, Pindel, Varscan2, at least 2 agree (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	F1 (indel only)	0.752
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	Vote ensemble Mutect2, Strelka, Pindel, Varscan2, at least 2 agree (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	Recall (indel only)	0.76
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	Vote ensemble Mutect2, Strelka, Pindel, Varscan2, at least 2 agree (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic indels (Guille et al. 2025 Table S7)	True positives (indel only)	38
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	Vote ensemble Lofreq, Muse, Mutect2, SomaticSniper, Strelka, Lancet, at least 3 agree (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7)	F1 (SNV only)	0.881
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	Vote ensemble Lofreq, Muse, Mutect2, SomaticSniper, Strelka, Lancet, at least 3 agree (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7)	False positives (SNV only)	58
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	Vote ensemble Lofreq, Muse, Mutect2, SomaticSniper, Strelka, Lancet, at least 3 agree (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7)	False positive rate (SNV only)	3.85e-7
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing; Guille et al. 2025, Supplementary Table S7 (validation dataset)	Vote ensemble Lofreq, Muse, Mutect2, SomaticSniper, Strelka, Lancet, at least 3 agree (Guille et al. 2025)	SEQC2 HCC1395 WES validation sample, somatic SNVs (Guille et al. 2025 Table S7)	Precision (SNV only)	0.943

In the other studies (40)
Study	Tool	Protocol or benchmark	Metric	Value
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	F1 (SNVs and indels, HG008 all-benchmark region)	0.776
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	False negatives (SNVs and indels, HG008 all-benchmark region)	6590
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	False positives (SNVs and indels, HG008 all-benchmark region)	133
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	Precision (SNVs and indels, HG008 all-benchmark region)	0.989
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	Recall (SNVs and indels, HG008 all-benchmark region)	0.638
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	True positives (SNVs and indels, HG008 all-benchmark region)	11600
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	F1 (indel only, HG008 primary region)	0.69
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	False negatives (indel only, HG008 primary region)	2320
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	False positives (indel only, HG008 primary region)	28
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	Recall (indel only, HG008 primary region)	0.529
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	True positives (indel only, HG008 primary region)	2610
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	F1 (SNVs and indels, HG008 primary region)	0.897
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	False negatives (SNVs and indels, HG008 primary region)	2510
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	False positives (SNVs and indels, HG008 primary region)	124
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	Precision (SNVs and indels, HG008 primary region)	0.989
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	Recall (SNVs and indels, HG008 primary region)	0.821
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	True positives (SNVs and indels, HG008 primary region)	11500
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV')	False negatives (SNV only, HG008 primary region)	186
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV')	False positives (SNV only, HG008 primary region)	96
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	DeepSomatic 1.10.0, bundled WGS model (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV')	Precision (SNV only, HG008 primary region)	0.989
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (Hasan 2026)	HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	F1 (SNVs and indels, HG008 all-benchmark region)	0.794
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Majority of Mutect2, Strelka2 and DeepSomatic (at least two callers) (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	F1 (SNVs and indels, HG008 primary region)	0.914
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (Hasan 2026)	HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	False positives (SNVs and indels, HG008 all-benchmark region)	7
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (Hasan 2026)	HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	Precision (SNVs and indels, HG008 all-benchmark region)	0.999
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (Hasan 2026)	HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	False positives (indel only, HG008 primary region)	2
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	False positives (SNVs and indels, HG008 primary region)	5
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	Precision (SNVs and indels, HG008 primary region)	1
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV')	False positives (SNV only, HG008 primary region)	3
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Strict intersection of Mutect2, Strelka2 and DeepSomatic (all three callers) (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV')	Precision (SNV only, HG008 primary region)	1
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (Hasan 2026)	HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	False negatives (SNVs and indels, HG008 all-benchmark region)	4710
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (Hasan 2026)	HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	Recall (SNVs and indels, HG008 all-benchmark region)	0.741
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (Hasan 2026)	HG008 all-benchmark region (sensitivity analysis), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 4)	True positives (SNVs and indels, HG008 all-benchmark region)	13500
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (Hasan 2026)	HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	F1 (indel only, HG008 primary region)	0.809
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (Hasan 2026)	HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	False negatives (indel only, HG008 primary region)	1080
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (Hasan 2026)	HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	Recall (indel only, HG008 primary region)	0.781
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (Hasan 2026)	HG008 primary region (nogermlineinterference), indels, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'INDEL')	True positives (indel only, HG008 primary region)	3860
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	False negatives (SNVs and indels, HG008 primary region)	1190
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	Recall (SNVs and indels, HG008 primary region)	0.915
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs and indels combined, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 1)	True positives (SNVs and indels, HG008 primary region)	12800
Prospectively frozen external benchmarking reveals benchmark-context dependence in somatic variant calling; AmbioSpire P003/T001 publication source data and reproducibility package v1.0.0 (Zenodo)	Union of Mutect2, Strelka2 and DeepSomatic (at least one caller) (Hasan 2026)	HG008 primary region (nogermlineinterference), SNVs, Mutect2, Strelka2, DeepSomatic and ensembles (Hasan 2026 Table 2, Class 'SNV')	False negatives (SNV only, HG008 primary region)	113

Follow-up

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