From: ISOWN: accurate somatic mutation identification in the absence of normal tissue controls
Dataset (source) | Number of samples | Number of samples used in testing | Mean read depth after filtering [95% CI] | Mutation calling pipeline | Total number of somatic/germline SNVsa in all samples | Mean somatic SNVs per sample [95% CI]a | Mean germline per sample [95% CI]a | Ratio somatic to germline (after collapsing) |
---|---|---|---|---|---|---|---|---|
UCEC (TGCA) | 251 | 151 | 88.84 [88.77, 88.92] | bambam_v1.4 | 38,012/504,241 | 147.015 [88.36, 205.66] | 2,008.92 [1,972.23, 2,045.62] | 2:1 |
BRCA (TCGA) | 500 | 400 | 85.92 [85.87, 85.97] | bambam_v1.4 | 5556/1,037,432 | 10.77 [9.05, 12.48] | 2,074.86 [2051.26, 2098.46] | 1:6 |
COAD (TGCA) | 215 | 115 | 122.17 [122.06, 122.28] | carnac_v1.0 | 60,624/1,932,510 | 276.68 [191.78, 361.58] | 8,988.41 [8826.01, 9150.82] | 1:1 |
KIRC (TGCA) | 304 | 204 | 177.59 [177.46, 177.73] | carnac_v1.0 | 10,489/2,416,155 | 33.56 [31.60, 35.51] | 7,947.87 [7792.68, 8,103.07] | 1:7 |
PAAD (TCGA) | 146 | 46 | 363.09 [362.80, 363.37] | carnac_v1.0 | 5,593/1,263,918 | 37.08 [33.59, 40.58] | 8,656.48 [8587.71, 8725.25] | 1:10.5 |
ESO (dbGAP) | 145 | 45 | 58.39 [58.33, 58.44] | MuTect2 | 26,098/790,051 | 181.85 [150.65, 213.05] | 5,451.51 [5,307.16, 5595.85] | 1:2.5 |