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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
78301-78350 / 86044 show all | |||||||||||||||
| ltrigg-rtg2 | SNP | * | map_l150_m0_e0 | * | 97.7647 | 95.7862 | 99.8267 | 65.0696 | 11525 | 507 | 11521 | 20 | 4 | 20.0000 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 78.8680 | 83.9810 | 74.3417 | 54.2249 | 2658 | 507 | 2654 | 916 | 914 | 99.7817 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 95.2832 | 91.6502 | 99.2161 | 44.8245 | 5565 | 507 | 5569 | 44 | 30 | 68.1818 | |
| cchapple-custom | SNP | tv | HG002complexvar | het | 99.7615 | 99.6630 | 99.8602 | 21.5432 | 150223 | 508 | 149954 | 210 | 146 | 69.5238 | |
| cchapple-custom | INDEL | D6_15 | * | hetalt | 0.0000 | 93.7852 | 0.0000 | 0.0000 | 7666 | 508 | 0 | 0 | 0 | ||
| ciseli-custom | SNP | ti | HG002compoundhet | homalt | 81.8243 | 93.1296 | 72.9667 | 35.5461 | 6886 | 508 | 6872 | 2546 | 564 | 22.1524 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.0410 | 96.8402 | 99.2720 | 68.1668 | 15569 | 508 | 15546 | 114 | 94 | 82.4561 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.0410 | 96.8402 | 99.2720 | 68.1668 | 15569 | 508 | 15546 | 114 | 94 | 82.4561 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 0.0000 | 95.4255 | 0.0000 | 0.0000 | 10597 | 508 | 0 | 0 | 0 | ||
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 80.6843 | 72.0726 | 91.6333 | 55.4102 | 1311 | 508 | 2749 | 251 | 244 | 97.2112 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 80.6843 | 72.0726 | 91.6333 | 55.4102 | 1311 | 508 | 2749 | 251 | 244 | 97.2112 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 83.2219 | 72.1186 | 98.3665 | 35.2346 | 1314 | 508 | 1385 | 23 | 22 | 95.6522 | |
| gduggal-snapvard | SNP | tv | map_l125_m2_e0 | * | 93.1565 | 96.9192 | 89.6752 | 79.7699 | 15981 | 508 | 15929 | 1834 | 123 | 6.7067 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.0502 | 96.8343 | 99.2971 | 55.9217 | 15539 | 508 | 15540 | 110 | 95 | 86.3636 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.0378 | 96.8281 | 99.2780 | 56.6258 | 15538 | 509 | 15539 | 113 | 101 | 89.3805 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 71.9347 | 56.7912 | 98.0910 | 82.9452 | 669 | 509 | 668 | 13 | 8 | 61.5385 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 62.3378 | 47.0343 | 92.4025 | 85.6385 | 452 | 509 | 450 | 37 | 14 | 37.8378 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.1790 | 86.6893 | 98.4109 | 40.6421 | 3315 | 509 | 3530 | 57 | 49 | 85.9649 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.5181 | 93.7722 | 99.4296 | 26.3580 | 7664 | 509 | 7670 | 44 | 43 | 97.7273 | |
| gduggal-snapvard | SNP | * | map_l150_m2_e1 | homalt | 97.6681 | 95.6963 | 99.7228 | 73.2280 | 11318 | 509 | 11153 | 31 | 25 | 80.6452 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 80.9438 | 72.3670 | 91.8269 | 61.8148 | 1333 | 509 | 1337 | 119 | 66 | 55.4622 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9263 | 98.3656 | 99.4933 | 72.9052 | 30634 | 509 | 30634 | 156 | 20 | 12.8205 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9263 | 98.3656 | 99.4933 | 72.9052 | 30634 | 509 | 30634 | 156 | 20 | 12.8205 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 83.9473 | 78.4628 | 90.2562 | 82.3482 | 1858 | 510 | 1973 | 213 | 125 | 58.6854 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 62.2829 | 56.8163 | 68.9135 | 42.3099 | 671 | 510 | 685 | 309 | 288 | 93.2039 | |
| astatham-gatk | INDEL | D1_5 | * | hetalt | 97.2343 | 95.0220 | 99.5520 | 63.2355 | 9735 | 510 | 9778 | 44 | 43 | 97.7273 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.9208 | 96.5506 | 97.2938 | 53.6376 | 14275 | 510 | 14273 | 397 | 386 | 97.2292 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.1341 | 96.7259 | 99.5838 | 73.0521 | 15067 | 510 | 15075 | 63 | 45 | 71.4286 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.6034 | 93.7599 | 99.6247 | 26.3649 | 7663 | 510 | 7699 | 29 | 29 | 100.0000 | |
| eyeh-varpipe | SNP | * | HG002complexvar | het | 99.8105 | 99.8904 | 99.7307 | 18.2348 | 464990 | 510 | 429610 | 1160 | 174 | 15.0000 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 21.7822 | 12.3499 | 92.2018 | 54.2977 | 72 | 511 | 201 | 17 | 17 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.5969 | 93.7477 | 99.6247 | 26.3674 | 7662 | 511 | 7698 | 29 | 29 | 100.0000 | |
| ckim-isaac | INDEL | D1_5 | map_l100_m2_e1 | * | 84.2482 | 73.6462 | 98.4160 | 83.3218 | 1428 | 511 | 1429 | 23 | 11 | 47.8261 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.2736 | 92.8150 | 100.0000 | 26.1913 | 6601 | 511 | 6645 | 0 | 0 | ||
| raldana-dualsentieon | SNP | tv | HG002compoundhet | * | 96.9959 | 94.2620 | 99.8931 | 47.1699 | 8411 | 512 | 8410 | 9 | 5 | 55.5556 | |
| gduggal-bwavard | SNP | ti | map_l100_m2_e0 | homalt | 98.5295 | 97.2036 | 99.8921 | 62.3227 | 17797 | 512 | 17597 | 19 | 15 | 78.9474 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.8830 | 96.2858 | 97.4877 | 51.4550 | 13273 | 512 | 13271 | 342 | 335 | 97.9532 | |
| ltrigg-rtg1 | SNP | ti | map_l100_m1_e0 | het | 99.0192 | 98.2900 | 99.7593 | 54.6205 | 29430 | 512 | 29432 | 71 | 7 | 9.8592 | |
| jli-custom | INDEL | D1_5 | HG002compoundhet | * | 97.1251 | 95.8153 | 98.4712 | 65.0788 | 11723 | 512 | 11723 | 182 | 174 | 95.6044 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 31.6644 | 21.5926 | 59.3458 | 76.4835 | 141 | 512 | 127 | 87 | 36 | 41.3793 | |
| gduggal-snapplat | SNP | * | map_l250_m0_e0 | * | 83.7909 | 76.0187 | 93.3333 | 96.5523 | 1623 | 512 | 1624 | 116 | 43 | 37.0690 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 90.9117 | 92.0249 | 89.8250 | 65.4470 | 5908 | 512 | 5853 | 663 | 643 | 96.9834 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 90.9117 | 92.0249 | 89.8250 | 65.4470 | 5908 | 512 | 5853 | 663 | 643 | 96.9834 | |
| gduggal-bwafb | SNP | * | HG002complexvar | homalt | 99.8832 | 99.8222 | 99.9441 | 19.8833 | 288062 | 513 | 288090 | 161 | 137 | 85.0932 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.5160 | 97.0969 | 97.9388 | 58.0884 | 17158 | 513 | 17153 | 361 | 342 | 94.7368 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.5160 | 97.0969 | 97.9388 | 58.0884 | 17158 | 513 | 17153 | 361 | 342 | 94.7368 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.6178 | 95.3805 | 99.9625 | 30.9240 | 10592 | 513 | 10671 | 4 | 3 | 75.0000 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 22.5181 | 16.0393 | 37.7778 | 69.3878 | 98 | 513 | 85 | 140 | 43 | 30.7143 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 54.6319 | 51.6463 | 57.9838 | 83.3700 | 549 | 514 | 788 | 571 | 15 | 2.6270 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 32.6838 | 19.8128 | 93.2836 | 48.6590 | 127 | 514 | 125 | 9 | 4 | 44.4444 | |