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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
31101-31150 / 86044 show all | |||||||||||||||
| gduggal-snapplat | SNP | * | map_l150_m2_e1 | het | 92.7489 | 92.3145 | 93.1874 | 87.6725 | 18798 | 1565 | 18822 | 1376 | 752 | 54.6512 | |
| jli-custom | INDEL | * | map_l100_m2_e1 | hetalt | 92.7483 | 87.1212 | 99.1525 | 87.2294 | 115 | 17 | 117 | 1 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 92.7463 | 87.9765 | 98.0630 | 55.8289 | 300 | 41 | 405 | 8 | 8 | 100.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.7461 | 88.4908 | 97.4313 | 66.6799 | 1630 | 212 | 1631 | 43 | 33 | 76.7442 | |
| ckim-isaac | SNP | ti | HG002complexvar | hetalt | 92.7461 | 86.4734 | 100.0000 | 28.1124 | 179 | 28 | 179 | 0 | 0 | ||
| gduggal-snapvard | INDEL | I1_5 | map_l250_m2_e1 | homalt | 92.7457 | 89.1304 | 96.6667 | 92.9742 | 41 | 5 | 58 | 2 | 1 | 50.0000 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 92.7440 | 88.1997 | 97.7819 | 39.9778 | 3356 | 449 | 1587 | 36 | 36 | 100.0000 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 92.7431 | 89.6335 | 96.0762 | 74.1823 | 856 | 99 | 857 | 35 | 22 | 62.8571 | |
| ghariani-varprowl | INDEL | I1_5 | * | het | 92.7410 | 98.8133 | 87.3718 | 65.8570 | 78102 | 938 | 78120 | 11291 | 10122 | 89.6466 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 92.7405 | 88.7846 | 97.0653 | 58.2458 | 8605 | 1087 | 8798 | 266 | 144 | 54.1353 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 92.7395 | 87.1028 | 99.1561 | 70.9914 | 466 | 69 | 470 | 4 | 3 | 75.0000 | |
| jpowers-varprowl | INDEL | I1_5 | map_l150_m2_e0 | het | 92.7393 | 90.9385 | 94.6128 | 92.4119 | 281 | 28 | 281 | 16 | 9 | 56.2500 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 92.7374 | 90.2174 | 95.4023 | 68.7050 | 83 | 9 | 83 | 4 | 3 | 75.0000 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 92.7368 | 97.8723 | 88.1133 | 66.0895 | 2162 | 47 | 2209 | 298 | 219 | 73.4899 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 92.7361 | 97.4125 | 88.4882 | 79.5170 | 640 | 17 | 638 | 83 | 78 | 93.9759 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.7350 | 99.3135 | 86.9739 | 48.2902 | 434 | 3 | 434 | 65 | 65 | 100.0000 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.7350 | 99.3135 | 86.9739 | 48.2902 | 434 | 3 | 434 | 65 | 65 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.7350 | 99.3135 | 86.9739 | 48.6097 | 434 | 3 | 434 | 65 | 65 | 100.0000 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 92.7348 | 88.8325 | 96.9957 | 40.7125 | 1050 | 132 | 226 | 7 | 7 | 100.0000 | |
| gduggal-snapfb | INDEL | * | map_l100_m0_e0 | * | 92.7347 | 91.6827 | 93.8111 | 85.2162 | 1433 | 130 | 1440 | 95 | 22 | 23.1579 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 92.7341 | 89.2791 | 96.4674 | 63.8560 | 13907 | 1670 | 13927 | 510 | 296 | 58.0392 | |
| astatham-gatk | SNP | tv | map_l250_m0_e0 | het | 92.7323 | 88.1119 | 97.8641 | 94.1324 | 504 | 68 | 504 | 11 | 2 | 18.1818 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | het | 92.7323 | 87.5000 | 98.6301 | 33.6364 | 21 | 3 | 144 | 2 | 1 | 50.0000 | |
| ckim-gatk | SNP | ti | map_l100_m1_e0 | het | 92.7314 | 88.0536 | 97.9342 | 80.4366 | 26365 | 3577 | 26358 | 556 | 60 | 10.7914 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.7289 | 88.8607 | 96.9493 | 47.5369 | 2449 | 307 | 2447 | 77 | 75 | 97.4026 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 92.7288 | 90.2597 | 95.3368 | 64.7810 | 556 | 60 | 552 | 27 | 25 | 92.5926 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.7273 | 86.4407 | 100.0000 | 73.8318 | 51 | 8 | 56 | 0 | 0 | ||
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 92.7273 | 89.4737 | 96.2264 | 99.5017 | 51 | 6 | 51 | 2 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.7273 | 86.4407 | 100.0000 | 72.6829 | 51 | 8 | 56 | 0 | 0 | ||
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.7273 | 86.4407 | 100.0000 | 73.9130 | 51 | 8 | 54 | 0 | 0 | ||
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.7263 | 88.4232 | 97.4697 | 64.7401 | 886 | 116 | 886 | 23 | 20 | 86.9565 | |
| astatham-gatk | SNP | * | map_l100_m0_e0 | * | 92.7245 | 86.6569 | 99.7057 | 72.7426 | 28459 | 4382 | 28455 | 84 | 35 | 41.6667 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.7242 | 88.2707 | 97.6510 | 77.3039 | 587 | 78 | 582 | 14 | 11 | 78.5714 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 92.7242 | 86.9159 | 99.3644 | 71.0961 | 465 | 70 | 469 | 3 | 3 | 100.0000 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 92.7237 | 93.5806 | 91.8824 | 43.4731 | 2624 | 180 | 2626 | 232 | 212 | 91.3793 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 92.7218 | 88.4618 | 97.4128 | 51.1450 | 15763 | 2056 | 30197 | 802 | 660 | 82.2943 | |
| gduggal-snapplat | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 92.7199 | 87.6559 | 98.4048 | 61.6199 | 8855 | 1247 | 8883 | 144 | 56 | 38.8889 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 92.7198 | 89.2857 | 96.4286 | 59.4203 | 25 | 3 | 27 | 1 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.7196 | 86.7545 | 99.5656 | 30.9538 | 1120 | 171 | 1146 | 5 | 4 | 80.0000 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 92.7176 | 99.4286 | 86.8552 | 76.5326 | 522 | 3 | 522 | 79 | 2 | 2.5317 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 92.7175 | 97.4908 | 88.3898 | 77.5276 | 1321 | 34 | 1279 | 168 | 162 | 96.4286 | |
| jpowers-varprowl | INDEL | I1_5 | HG002complexvar | * | 92.7158 | 90.8192 | 94.6934 | 52.3150 | 30300 | 3063 | 30175 | 1691 | 1600 | 94.6186 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 92.7152 | 99.5261 | 86.7769 | 70.8785 | 210 | 1 | 210 | 32 | 32 | 100.0000 | |
| jmaeng-gatk | SNP | ti | map_l100_m2_e0 | het | 92.7126 | 88.1229 | 97.8066 | 81.8391 | 26985 | 3637 | 26978 | 605 | 56 | 9.2562 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.7110 | 86.7096 | 99.6050 | 29.5781 | 1481 | 227 | 1513 | 6 | 6 | 100.0000 | |
| jlack-gatk | INDEL | * | map_l100_m1_e0 | hetalt | 92.7075 | 87.0968 | 99.0909 | 87.3418 | 108 | 16 | 109 | 1 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | * | map_l100_m2_e0 | hetalt | 92.7039 | 86.4000 | 100.0000 | 88.0952 | 108 | 17 | 110 | 0 | 0 | ||
| gduggal-snapplat | SNP | * | map_l150_m2_e0 | het | 92.7026 | 92.2615 | 93.1480 | 87.6370 | 18575 | 1558 | 18597 | 1368 | 748 | 54.6784 | |
| jpowers-varprowl | INDEL | * | map_l125_m0_e0 | het | 92.6995 | 93.0153 | 92.3858 | 91.5475 | 546 | 41 | 546 | 45 | 27 | 60.0000 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 92.6984 | 90.4665 | 95.0431 | 49.8920 | 446 | 47 | 441 | 23 | 12 | 52.1739 | |