Protocol

SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)

Indel F1 per replicate pair for nine callers and eight NeuSomatic models.

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Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample · Original source · Genome Biology 23:12, published 2022-01-07; PMC8740374 full-text XML
Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Original source · 13059_2021_2592_MOESM2_ESM.pdf

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Technical metadata and extraction receipts

Stable ID: somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

areas: dna-genomes
contexts: clinical_research
protocol: Paired tumour-normal calling of each replicate pair; PASS calls scored by exact match. All callers and models were scored on the 50% of the SEQC2 high-confidence genome held out from SEQC-WGS-GT-50 training (about 1.4 Gb; about 21K truth SNVs and 1.3K truth indels), against SEQC2 HighConf and MedConf calls (v1.0), LowConf calls blacklisted and ambiguous private calls excluded.
version: Additional file 2 Table S2
metric: f1-score
limitations: Developer paper: the authors developed NeuSomatic (two hold a patent application on it; Competing interests) and trained and selected every NeuSomatic model; NeuSomatic rows are author_reported.; One cell-line pair (HCC1395/HCC1395BL). The SEQC2 truth set (v1.0, 39,536 SNVs and 2,020 indels) was built by the SEQC2 somatic working group, whose reference papers have co-authors W. Xiao and L. T. Fang as first authors, with the SomaticSeq classifier, which co-authors L. T. Fang and M. Mohiyuddin helped develop (references 2, 3 and 20). It has a 5% VAF and 50x depth detection limit, LowConf calls are blacklisted, and ambiguous private calls are excluded from scoring (Methods 'Evaluation process').; Scored on the 50% of the high-confidence genome held out from SEQC-WGS-GT-50 training (about 21K truth SNVs and 1.3K truth indels). The NeuSomatic and NeuSomatic-S SEQC-WGS-Spike, SEQC-WGS-GT-50 and SEQC-WGS-GT50-SpikeWGS10 models were trained on this cell line and are excluded from this judgement, as is Octopus-RF, whose forest is not identified. The DREAM3 models, trained on DREAM Challenge Stage 3 data, are kept.; The NeuSomatic ensemble mode takes calls from MuTect2, SomaticSniper, Strelka2, MuSE and VarDict as input channels.; Only F1 is printed; no precision, recall or uncertainty in these tables.; Caller versions as in Methods (for example MuTect2 4.beta.6, Strelka2 2.8.4, Lancet 1.0.7, NeuSomatic 0.1.4).; Results say 21 replicates from six sequencing centres; the row labels carry seven site codes (IL and NV are probably both Illumina).; Rows are WGS replicate pairs from the set the SEQC2 models were trained on (seven pairs from six centres plus a merged NovaSeq pair; spike-in models on HCC1395BL replicates from four sites); the paper does not say which of the 21 pairs.; SomaticSniper and MuSE do not call indels ('-' in the table).
source locator: Additional file 2 Table S2 (INDELs section); Methods 'Evaluation process'

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	81.7% F1 (INDELs, average over the 21 replicate pairs as printed) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'Average', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	80.5% F1 (INDELs, tumour WGS_EA_T_1 with normal WGS_EA_N_1) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_EA_T_1 vs WGS_EA_N_1', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	78.8% F1 (INDELs, tumour WGS_FD_T_1 with normal WGS_FD_N_1) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_FD_T_1 vs WGS_FD_N_1', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	78.5% F1 (INDELs, tumour WGS_FD_T_2 with normal WGS_FD_N_2) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_FD_T_2 vs WGS_FD_N_2', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	78.9% F1 (INDELs, tumour WGS_FD_T_3 with normal WGS_FD_N_3) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_FD_T_3 vs WGS_FD_N_3', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	86.3% F1 (INDELs, tumour WGS_IL_T_1 with normal WGS_IL_N_1) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_IL_T_1 vs WGS_IL_N_1', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	83.2% F1 (INDELs, tumour WGS_IL_T_2 with normal WGS_IL_N_2) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_IL_T_2 vs WGS_IL_N_2', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	83.9% F1 (INDELs, tumour WGS_IL_T_3 with normal WGS_IL_N_3) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_IL_T_3 vs WGS_IL_N_3', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	82.6% F1 (INDELs, tumour WGS_LL_T_1 with normal WGS_LL_N_1) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_LL_T_1 vs WGS_LL_N_1', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	83% F1 (INDELs, tumour WGS_NC_T_1 with normal WGS_NC_N_1) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_NC_T_1 vs WGS_NC_N_1', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	81.1% F1 (INDELs, tumour WGS_NS_T_1 with normal WGS_NS_N_1) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_NS_T_1 vs WGS_NS_N_1', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	80.9% F1 (INDELs, tumour WGS_NS_T_2 with normal WGS_NS_N_2) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_NS_T_2 vs WGS_NS_N_2', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	80.2% F1 (INDELs, tumour WGS_NS_T_3 with normal WGS_NS_N_3) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_NS_T_3 vs WGS_NS_N_3', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	81.6% F1 (INDELs, tumour WGS_NS_T_4 with normal WGS_NS_N_4) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_NS_T_4 vs WGS_NS_N_4', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	79.4% F1 (INDELs, tumour WGS_NS_T_5 with normal WGS_NS_N_5) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_NS_T_5 vs WGS_NS_N_5', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	81.4% F1 (INDELs, tumour WGS_NS_T_6 with normal WGS_NS_N_6) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_NS_T_6 vs WGS_NS_N_6', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	80.3% F1 (INDELs, tumour WGS_NS_T_7 with normal WGS_NS_N_7) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_NS_T_7 vs WGS_NS_N_7', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	79.9% F1 (INDELs, tumour WGS_NS_T_8 with normal WGS_NS_N_8) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_NS_T_8 vs WGS_NS_N_8', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	81.1% F1 (INDELs, tumour WGS_NS_T_9 with normal WGS_NS_N_9) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_NS_T_9 vs WGS_NS_N_9', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	84.6% F1 (INDELs, tumour WGS_NV_T_1 with normal WGS_NV_N_1) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_NV_T_1 vs WGS_NV_N_1', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	83.8% F1 (INDELs, tumour WGS_NV_T_2 with normal WGS_NV_N_2) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_NV_T_2 vs WGS_NV_N_2', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	85.2% F1 (INDELs, tumour WGS_NV_T_3 with normal WGS_NV_N_3) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_NV_T_3 vs WGS_NV_N_3', column 'DRAGEN'
Configuration: Lancet 1.0.7 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	77.7% F1 (INDELs, average over the 21 replicate pairs as printed) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Lancet on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'Average', column 'Lancet'
Configuration: Lancet 1.0.7 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	76.2% F1 (INDELs, tumour WGS_EA_T_1 with normal WGS_EA_N_1) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Lancet on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_EA_T_1 vs WGS_EA_N_1', column 'Lancet'
Configuration: Lancet 1.0.7 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2) Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	77.3% F1 (INDELs, tumour WGS_FD_T_1 with normal WGS_FD_N_1) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Lancet on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S2, INDELs section, row 'WGS_FD_T_1 vs WGS_FD_N_1', column 'Lancet'