Configuration

SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)

SomaticSniper as run in the cited comparison.

Overview

SomaticSniper: Somatic SNV caller using joint genotype analysis.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

3 evaluations · 77 results. Different protocols are not a single leaderboard.

Sorted by F1 (SNVs, average over the 21 replicate pairs as printed) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	F1 (SNVs, average over the 21 replicate pairs as printed)	F1 (SNVs, average over the 47 purity-coverage pairs as printed)	F1 (SNVs, average over the 6 library pairs as printed)	F1 (SNVs, tumour LBP_Nextera_T_100ng with normal LBP_Nextera_N_100ng)	F1 (SNVs, tumour LBP_Nextera_T_10ng with normal LBP_Nextera_N_10ng)	F1 (SNVs, tumour LBP_Nextera_T_1ng with normal LBP_Nextera_N_1ng)	F1 (SNVs, tumour LBP_TruSeq_T_100ng with normal LBP_TruSeq_N_100ng)	F1 (SNVs, tumour LBP_TruSeq_T_10ng with normal LBP_TruSeq_N_10ng)	F1 (SNVs, tumour LBP_TruSeq_T_1ng with normal LBP_TruSeq_N_1ng)	F1 (SNVs, tumour SPP_100x_10%T with normal SPP_100x_100%N)	F1 (SNVs, tumour SPP_100x_100%T with normal SPP_100x_100%N)	F1 (SNVs, tumour SPP_100x_20%T with normal SPP_100x_100%N)	F1 (SNVs, tumour SPP_100x_5%T with normal SPP_100x_100%N)	F1 (SNVs, tumour SPP_100x_50%T with normal SPP_100x_100%N)	F1 (SNVs, tumour SPP_100x_75%T with normal SPP_100x_100%N)	F1 (SNVs, tumour SPP_10x_10%T with normal SPP_10x_100%N)	F1 (SNVs, tumour SPP_10x_100%T with normal SPP_10x_100%N)	F1 (SNVs, tumour SPP_10x_20%T with normal SPP_10x_100%N)	F1 (SNVs, tumour SPP_10x_5%T with normal SPP_10x_100%N)	F1 (SNVs, tumour SPP_10x_50%T with normal SPP_10x_100%N)	F1 (SNVs, tumour SPP_10x_75%T with normal SPP_10x_100%N)	F1 (SNVs, tumour SPP_200x_10%T with normal SPP_200x_100%N)	F1 (SNVs, tumour SPP_200x_100%T with normal SPP_200x_100%N)	F1 (SNVs, tumour SPP_200x_20%T with normal SPP_200x_100%N)	F1 (SNVs, tumour SPP_200x_5%T with normal SPP_200x_100%N)	F1 (SNVs, tumour SPP_200x_50%T with normal SPP_200x_100%N)	F1 (SNVs, tumour SPP_200x_75%T with normal SPP_200x_100%N)	F1 (SNVs, tumour SPP_300x_10%T with normal SPP_300x_100%N)	F1 (SNVs, tumour SPP_300x_100%T with normal SPP_300x_100%N)	F1 (SNVs, tumour SPP_300x_20%T with normal SPP_300x_100%N)	F1 (SNVs, tumour SPP_300x_5%T with normal SPP_300x_100%N)	F1 (SNVs, tumour SPP_300x_50%T with normal SPP_300x_100%N)	F1 (SNVs, tumour SPP_300x_75%T with normal SPP_300x_100%N)	F1 (SNVs, tumour SPP_30x_10%T with normal SPP_30x_100%N)	F1 (SNVs, tumour SPP_30x_100%T with normal SPP_30x_100%N)	F1 (SNVs, tumour SPP_30x_20%T with normal SPP_30x_100%N)	F1 (SNVs, tumour SPP_30x_5%T with normal SPP_30x_100%N)	F1 (SNVs, tumour SPP_30x_50%T with normal SPP_30x_100%N)	F1 (SNVs, tumour SPP_30x_75%T with normal SPP_30x_100%N)	F1 (SNVs, tumour SPP_50x_10%T with normal SPP_50x_100%N)	F1 (SNVs, tumour SPP_50x_100%T with normal SPP_50x_100%N)	F1 (SNVs, tumour SPP_50x_20%T with normal SPP_50x_100%N)	F1 (SNVs, tumour SPP_50x_5%T with normal SPP_50x_100%N)	F1 (SNVs, tumour SPP_50x_50%T with normal SPP_50x_100%N)	F1 (SNVs, tumour SPP_50x_75%T with normal SPP_50x_100%N)	F1 (SNVs, tumour SPP_80x_10%T with normal SPP_80x_100%N)	F1 (SNVs, tumour SPP_80x_10%T with normal SPP_80x_95%N)	F1 (SNVs, tumour SPP_80x_100%T with normal SPP_80x_100%N)	F1 (SNVs, tumour SPP_80x_100%T with normal SPP_80x_95%N)	F1 (SNVs, tumour SPP_80x_20%T with normal SPP_80x_100%N)	F1 (SNVs, tumour SPP_80x_20%T with normal SPP_80x_95%N)	F1 (SNVs, tumour SPP_80x_5%T with normal SPP_80x_100%N)	F1 (SNVs, tumour SPP_80x_50%T with normal SPP_80x_100%N)	F1 (SNVs, tumour SPP_80x_50%T with normal SPP_80x_95%N)	F1 (SNVs, tumour SPP_80x_75%T with normal SPP_80x_100%N)	F1 (SNVs, tumour SPP_80x_75%T with normal SPP_80x_95%N)	F1 (SNVs, tumour WGS_EA_T_1 with normal WGS_EA_N_1)	F1 (SNVs, tumour WGS_FD_T_1 with normal WGS_FD_N_1)	F1 (SNVs, tumour WGS_FD_T_2 with normal WGS_FD_N_2)	F1 (SNVs, tumour WGS_FD_T_3 with normal WGS_FD_N_3)	F1 (SNVs, tumour WGS_IL_T_1 with normal WGS_IL_N_1)	F1 (SNVs, tumour WGS_IL_T_2 with normal WGS_IL_N_2)	F1 (SNVs, tumour WGS_IL_T_3 with normal WGS_IL_N_3)	F1 (SNVs, tumour WGS_LL_T_1 with normal WGS_LL_N_1)	F1 (SNVs, tumour WGS_NC_T_1 with normal WGS_NC_N_1)	F1 (SNVs, tumour WGS_NS_T_1 with normal WGS_NS_N_1)	F1 (SNVs, tumour WGS_NS_T_2 with normal WGS_NS_N_2)	F1 (SNVs, tumour WGS_NS_T_3 with normal WGS_NS_N_3)	F1 (SNVs, tumour WGS_NS_T_4 with normal WGS_NS_N_4)	F1 (SNVs, tumour WGS_NS_T_5 with normal WGS_NS_N_5)	F1 (SNVs, tumour WGS_NS_T_6 with normal WGS_NS_N_6)	F1 (SNVs, tumour WGS_NS_T_7 with normal WGS_NS_N_7)	F1 (SNVs, tumour WGS_NS_T_8 with normal WGS_NS_N_8)	F1 (SNVs, tumour WGS_NS_T_9 with normal WGS_NS_N_9)	F1 (SNVs, tumour WGS_NV_T_1 with normal WGS_NV_N_1)	F1 (SNVs, tumour WGS_NV_T_2 with normal WGS_NV_N_2)	F1 (SNVs, tumour WGS_NV_T_3 with normal WGS_NV_N_3)
SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)Evaluation	SEQC2 HCC1395 sequencing centre and platform, SNV F1 (Sahraeian et al. 2022 Table S2), SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres	67.3%	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	65.1%	68.4%	67.5%	66.8%	67.5%	68.5%	68.6%	69.7%	68.2%	67.4%	69.1%	68.1%	68.2%	67.3%	67.3%	68.3%	69.3%	68.8%	62.7%	62.7%	63.4%
SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)Evaluation	SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4), SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA)	Not reported	Not reported	58%	66.3%	62.5%	63.1%	67.5%	68.6%	20.2%	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)Evaluation	SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3), SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	Not reported	33.7%	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	5.9%	60.8%	30%	0.5%	60.5%	61.3%	1%	32.5%	4.5%	0.2%	18.9%	27.7%	2.4%	57.5%	22.9%	0.1%	55.8%	57.1%	1.3%	56.4%	18.4%	0%	55.5%	57.6%	5.9%	69.8%	24.8%	0.8%	60.1%	68.3%	6.5%	65.3%	28.9%	0.9%	61.6%	65.2%	6.5%	4.7%	62.4%	62.8%	30%	25.7%	0.6%	61%	58.6%	62.4%	61.3%	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported

All 77 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4) Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA)	58% F1 (SNVs, average over the 6 library 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 SomaticSniper on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-snv 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 S4, SNVs section, row 'Average', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4) Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA)	66.3% F1 (SNVs, tumour LBP_Nextera_T_100ng with normal LBP_Nextera_N_100ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-snv 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 S4, SNVs section, row 'LBP_Nextera_T_100ng vs LBP_Nextera_N_100ng', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4) Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA)	62.5% F1 (SNVs, tumour LBP_Nextera_T_10ng with normal LBP_Nextera_N_10ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-snv 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 S4, SNVs section, row 'LBP_Nextera_T_10ng vs LBP_Nextera_N_10ng', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4) Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA)	63.1% F1 (SNVs, tumour LBP_Nextera_T_1ng with normal LBP_Nextera_N_1ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-snv 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 S4, SNVs section, row 'LBP_Nextera_T_1ng vs LBP_Nextera_N_1ng', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4) Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA)	67.5% F1 (SNVs, tumour LBP_TruSeq_T_100ng with normal LBP_TruSeq_N_100ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-snv 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 S4, SNVs section, row 'LBP_TruSeq_T_100ng vs LBP_TruSeq_N_100ng', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4) Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA)	68.6% F1 (SNVs, tumour LBP_TruSeq_T_10ng with normal LBP_TruSeq_N_10ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-snv 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 S4, SNVs section, row 'LBP_TruSeq_T_10ng vs LBP_TruSeq_N_10ng', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4) Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA)	20.2% F1 (SNVs, tumour LBP_TruSeq_T_1ng with normal LBP_TruSeq_N_1ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-snv 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 S4, SNVs section, row 'LBP_TruSeq_T_1ng vs LBP_TruSeq_N_1ng', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	33.7% F1 (SNVs, average over the 47 purity-coverage 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 SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'Average', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	5.9% F1 (SNVs, tumour SPP_100x_10%T with normal SPP_100x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_100x_10%T vs SPP_100x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	60.8% F1 (SNVs, tumour SPP_100x_100%T with normal SPP_100x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_100x_100%T vs SPP_100x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	30% F1 (SNVs, tumour SPP_100x_20%T with normal SPP_100x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_100x_20%T vs SPP_100x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	0.5% F1 (SNVs, tumour SPP_100x_5%T with normal SPP_100x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_100x_5%T vs SPP_100x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	60.5% F1 (SNVs, tumour SPP_100x_50%T with normal SPP_100x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_100x_50%T vs SPP_100x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	61.3% F1 (SNVs, tumour SPP_100x_75%T with normal SPP_100x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_100x_75%T vs SPP_100x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	1% F1 (SNVs, tumour SPP_10x_10%T with normal SPP_10x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_10x_10%T vs SPP_10x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	32.5% F1 (SNVs, tumour SPP_10x_100%T with normal SPP_10x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_10x_100%T vs SPP_10x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	4.5% F1 (SNVs, tumour SPP_10x_20%T with normal SPP_10x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_10x_20%T vs SPP_10x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	0.2% F1 (SNVs, tumour SPP_10x_5%T with normal SPP_10x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_10x_5%T vs SPP_10x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	18.9% F1 (SNVs, tumour SPP_10x_50%T with normal SPP_10x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_10x_50%T vs SPP_10x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	27.7% F1 (SNVs, tumour SPP_10x_75%T with normal SPP_10x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_10x_75%T vs SPP_10x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	2.4% F1 (SNVs, tumour SPP_200x_10%T with normal SPP_200x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_200x_10%T vs SPP_200x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	57.5% F1 (SNVs, tumour SPP_200x_100%T with normal SPP_200x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_200x_100%T vs SPP_200x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	22.9% F1 (SNVs, tumour SPP_200x_20%T with normal SPP_200x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_200x_20%T vs SPP_200x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	0.1% F1 (SNVs, tumour SPP_200x_5%T with normal SPP_200x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_200x_5%T vs SPP_200x_100%N', column 'SomaticSniper'
Configuration: SomaticSniper 1.0.5.0 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	55.8% F1 (SNVs, tumour SPP_200x_50%T with normal SPP_200x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SomaticSniper on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv 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 S3, SNVs section, row 'SPP_200x_50%T vs SPP_200x_100%N', column 'SomaticSniper'

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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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Stable ID: somatic-neusomatic-20261010-config-sahraeian2022-somaticsniper

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: SomaticSniper
foundation model eligible: false
version: 1.0.5.0
protocol: Parameters -q 1 -Q 15 -s 1e-05; PASS calls
source locator: Methods 'Somatic mutation detection algorithms'; Additional file 2 Table S1 and Tables S2-S4 column headers

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