PrecisionFDA
Truth Challenge
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Explore HG002 comparison results
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| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
59851-59900 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 91.3157 | 84.9354 | 98.7324 | 37.8284 | 592 | 105 | 701 | 9 | 9 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.0288 | 97.3348 | 98.7327 | 54.0492 | 21657 | 593 | 21658 | 278 | 267 | 96.0432 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 95.2682 | 92.0384 | 98.7330 | 37.3051 | 1630 | 141 | 2104 | 27 | 26 | 96.2963 | |
| hfeng-pmm2 | SNP | * | map_l150_m2_e1 | het | 98.9487 | 99.1652 | 98.7332 | 79.6403 | 20193 | 170 | 20187 | 259 | 23 | 8.8803 | |
| jpowers-varprowl | SNP | ti | map_l100_m1_e0 | * | 98.2270 | 97.7259 | 98.7332 | 68.5176 | 46841 | 1090 | 46843 | 601 | 190 | 31.6140 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 96.3092 | 94.0011 | 98.7334 | 63.5924 | 1661 | 106 | 1637 | 21 | 7 | 33.3333 | |
| gduggal-snapplat | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 91.7792 | 85.7399 | 98.7338 | 51.3537 | 3349 | 557 | 3353 | 43 | 4 | 9.3023 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.2868 | 95.8815 | 98.7340 | 45.9174 | 14015 | 602 | 39539 | 507 | 431 | 85.0099 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.1647 | 97.6017 | 98.7342 | 72.8055 | 936 | 23 | 936 | 12 | 8 | 66.6667 | |
| asubramanian-gatk | INDEL | D6_15 | map_l150_m2_e1 | * | 94.4860 | 90.5882 | 98.7342 | 94.0242 | 77 | 8 | 78 | 1 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 98.5228 | 98.3122 | 98.7342 | 24.0385 | 233 | 4 | 234 | 3 | 3 | 100.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | map_siren | hetalt | 95.7055 | 92.8571 | 98.7342 | 91.2804 | 78 | 6 | 78 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | SNP | * | map_siren | hetalt | 97.5000 | 96.2963 | 98.7342 | 67.0833 | 78 | 3 | 78 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | SNP | tv | map_siren | hetalt | 97.5000 | 96.2963 | 98.7342 | 67.0833 | 78 | 3 | 78 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | SNP | tv | map_siren | hetalt | 97.5000 | 96.2963 | 98.7342 | 67.4897 | 78 | 3 | 78 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | SNP | * | map_siren | hetalt | 97.5000 | 96.2963 | 98.7342 | 67.4897 | 78 | 3 | 78 | 1 | 1 | 100.0000 | |
| jli-custom | SNP | tv | map_l250_m1_e0 | het | 97.3617 | 96.0269 | 98.7342 | 85.3704 | 1716 | 71 | 1716 | 22 | 7 | 31.8182 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 89.1429 | 81.2500 | 98.7342 | 66.3830 | 156 | 36 | 156 | 2 | 2 | 100.0000 | |
| gduggal-bwavard | INDEL | D1_5 | map_l150_m0_e0 | homalt | 96.3707 | 94.1176 | 98.7342 | 87.7519 | 80 | 5 | 78 | 1 | 1 | 100.0000 | |
| gduggal-snapfb | INDEL | D1_5 | func_cds | * | 98.4227 | 98.1132 | 98.7342 | 40.6015 | 156 | 3 | 156 | 2 | 1 | 50.0000 | |
| cchapple-custom | INDEL | D1_5 | map_l150_m0_e0 | homalt | 96.3707 | 94.1176 | 98.7342 | 89.6053 | 80 | 5 | 78 | 1 | 1 | 100.0000 | |
| cchapple-custom | SNP | * | tech_badpromoters | homalt | 98.7421 | 98.7500 | 98.7342 | 44.3662 | 79 | 1 | 78 | 1 | 1 | 100.0000 | |
| ckim-dragen | SNP | tv | func_cds | * | 99.3521 | 99.9771 | 98.7347 | 37.1039 | 4370 | 1 | 4370 | 56 | 0 | 0.0000 | |
| jmaeng-gatk | SNP | * | map_siren | * | 94.0415 | 89.7742 | 98.7347 | 67.2383 | 131275 | 14953 | 131252 | 1682 | 121 | 7.1938 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.6974 | 98.6597 | 98.7351 | 66.8148 | 2650 | 36 | 2654 | 34 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.9007 | 95.1331 | 98.7352 | 48.1982 | 1251 | 64 | 1249 | 16 | 11 | 68.7500 | |
| jpowers-varprowl | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.3232 | 99.9179 | 98.7356 | 57.1091 | 6083 | 5 | 6091 | 78 | 58 | 74.3590 | |
| rpoplin-dv42 | SNP | tv | map_l150_m2_e1 | het | 98.8030 | 98.8704 | 98.7357 | 75.2106 | 7265 | 83 | 7263 | 93 | 49 | 52.6882 | |
| dgrover-gatk | SNP | ti | map_l250_m2_e1 | * | 98.6193 | 98.5028 | 98.7362 | 90.4249 | 5000 | 76 | 5000 | 64 | 18 | 28.1250 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.2878 | 93.9576 | 98.7365 | 52.3236 | 3281 | 211 | 3282 | 42 | 37 | 88.0952 | |
| gduggal-bwaplat | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 92.0320 | 86.1800 | 98.7365 | 71.8190 | 15384 | 2467 | 15395 | 197 | 56 | 28.4264 | |
| ckim-isaac | INDEL | I16_PLUS | * | hetalt | 65.0682 | 48.5224 | 98.7366 | 42.1910 | 1018 | 1080 | 1016 | 13 | 11 | 84.6154 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.8868 | 97.0512 | 98.7368 | 59.9494 | 1876 | 57 | 1876 | 24 | 23 | 95.8333 | |
| rpoplin-dv42 | SNP | * | map_l150_m0_e0 | * | 98.4495 | 98.1632 | 98.7374 | 78.1997 | 11811 | 221 | 11808 | 151 | 101 | 66.8874 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.7421 | 98.7469 | 98.7374 | 50.0631 | 394 | 5 | 391 | 5 | 5 | 100.0000 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9134 | 97.1029 | 98.7375 | 60.0294 | 1877 | 56 | 1877 | 24 | 23 | 95.8333 | |
| rpoplin-dv42 | SNP | tv | map_l100_m0_e0 | * | 98.7643 | 98.7911 | 98.7375 | 67.3276 | 10950 | 134 | 10949 | 140 | 63 | 45.0000 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 72.4268 | 57.1879 | 98.7375 | 38.9205 | 1452 | 1087 | 1486 | 19 | 19 | 100.0000 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.4252 | 92.3274 | 98.7380 | 54.1740 | 3598 | 299 | 3599 | 46 | 39 | 84.7826 | |
| gduggal-bwavard | INDEL | I6_15 | HG002complexvar | homalt | 84.0374 | 73.1466 | 98.7385 | 35.6458 | 888 | 326 | 861 | 11 | 9 | 81.8182 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.1387 | 99.5421 | 98.7386 | 58.2561 | 3913 | 18 | 3914 | 50 | 1 | 2.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.2888 | 95.8808 | 98.7387 | 78.3161 | 1094 | 47 | 1096 | 14 | 11 | 78.5714 | |
| dgrover-gatk | SNP | ti | map_l250_m2_e0 | * | 98.6206 | 98.5024 | 98.7390 | 90.3671 | 4933 | 75 | 4933 | 63 | 18 | 28.5714 | |
| hfeng-pmm3 | INDEL | * | map_l100_m2_e0 | het | 98.4803 | 98.2228 | 98.7391 | 83.7628 | 2266 | 41 | 2271 | 29 | 5 | 17.2414 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 97.5587 | 96.4058 | 98.7395 | 42.1025 | 3326 | 124 | 3290 | 42 | 14 | 33.3333 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 97.7062 | 96.6942 | 98.7395 | 67.2176 | 234 | 8 | 235 | 3 | 2 | 66.6667 | |
| gduggal-snapvard | SNP | tv | segdup | * | 97.9096 | 97.0933 | 98.7396 | 94.2289 | 8284 | 248 | 8226 | 105 | 33 | 31.4286 | |
| hfeng-pmm3 | INDEL | * | map_l125_m2_e1 | * | 98.5832 | 98.4270 | 98.7399 | 86.2184 | 2190 | 35 | 2194 | 28 | 6 | 21.4286 | |
| bgallagher-sentieon | INDEL | I1_5 | map_l125_m2_e1 | * | 98.7952 | 98.8506 | 98.7400 | 87.1353 | 860 | 10 | 862 | 11 | 2 | 18.1818 | |
| bgallagher-sentieon | INDEL | D1_5 | map_siren | het | 99.1706 | 99.6047 | 98.7402 | 81.3769 | 2268 | 9 | 2273 | 29 | 2 | 6.8966 | |