| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 59.2% F1 (INDELs, average over the 47 purity-coverage pairs as printed) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'Average', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 49.9% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_100x_10%T vs SPP_100x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 85.6% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_100x_100%T vs SPP_100x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 72.4% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_100x_20%T vs SPP_100x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 26.3% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_100x_5%T vs SPP_100x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 83% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_100x_50%T vs SPP_100x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 84.8% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_100x_75%T vs SPP_100x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 3.6% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_10x_10%T vs SPP_10x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 58.8% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_10x_100%T vs SPP_10x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 13.8% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_10x_20%T vs SPP_10x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 1.2% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_10x_5%T vs SPP_10x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 41.3% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_10x_50%T vs SPP_10x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 53.6% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_10x_75%T vs SPP_10x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 63.2% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_200x_10%T vs SPP_200x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 85.2% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_200x_100%T vs SPP_200x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 76.7% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_200x_20%T vs SPP_200x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 38.9% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_200x_5%T vs SPP_200x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 83.1% F1 (INDELs, 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 | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_200x_50%T vs SPP_200x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 84.5% F1 (INDELs, tumour SPP_200x_75%T with normal SPP_200x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_200x_75%T vs SPP_200x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 63.8% F1 (INDELs, tumour SPP_300x_10%T with normal SPP_300x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_300x_10%T vs SPP_300x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 84.4% F1 (INDELs, tumour SPP_300x_100%T with normal SPP_300x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_300x_100%T vs SPP_300x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 75% F1 (INDELs, tumour SPP_300x_20%T with normal SPP_300x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_300x_20%T vs SPP_300x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 44.1% F1 (INDELs, tumour SPP_300x_5%T with normal SPP_300x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_300x_5%T vs SPP_300x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 82.9% F1 (INDELs, tumour SPP_300x_50%T with normal SPP_300x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_300x_50%T vs SPP_300x_100%N', column 'Octopus-RF' |
|---|
| Configuration: Octopus-RF v0.7.4 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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 | 83.5% F1 (INDELs, tumour SPP_300x_75%T with normal SPP_300x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceOctopus-RF on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_300x_75%T vs SPP_300x_100%N', column 'Octopus-RF' |
|---|