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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
79301-79350 / 86044 show all | |||||||||||||||
| gduggal-snapvard | SNP | ti | map_l125_m1_e0 | homalt | 97.8107 | 95.9258 | 99.7712 | 66.1153 | 10595 | 450 | 10464 | 24 | 19 | 79.1667 | |
| 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 | ||
| astatham-gatk | SNP | * | map_l150_m0_e0 | * | 93.4108 | 88.0735 | 99.4368 | 82.7630 | 10597 | 1435 | 10594 | 60 | 21 | 35.0000 | |
| ndellapenna-hhga | INDEL | I1_5 | HG002compoundhet | hetalt | 97.1229 | 94.8287 | 99.5310 | 57.0294 | 10599 | 578 | 10611 | 50 | 44 | 88.0000 | |
| mlin-fermikit | SNP | * | segdup | homalt | 98.6182 | 98.6689 | 98.5676 | 86.0366 | 10600 | 143 | 10597 | 154 | 135 | 87.6623 | |
| gduggal-snapfb | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 89.9321 | 98.7700 | 82.5458 | 58.4226 | 10600 | 132 | 10674 | 2257 | 114 | 5.0510 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.6600 | 95.4525 | 99.9719 | 30.6839 | 10600 | 505 | 10680 | 3 | 2 | 66.6667 | |
| anovak-vg | SNP | * | segdup | homalt | 98.7938 | 98.6875 | 98.9004 | 87.8317 | 10602 | 141 | 10523 | 117 | 108 | 92.3077 | |
| hfeng-pmm2 | INDEL | I1_5 | * | hetalt | 97.2753 | 94.7119 | 99.9812 | 62.6532 | 10603 | 592 | 10662 | 2 | 2 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | * | hetalt | 97.2805 | 94.7387 | 99.9625 | 62.4322 | 10606 | 589 | 10669 | 4 | 4 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | * | het | 91.7291 | 91.4941 | 91.9653 | 44.9050 | 10606 | 986 | 10084 | 881 | 656 | 74.4608 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.5419 | 95.5335 | 99.6365 | 30.2678 | 10609 | 496 | 10690 | 39 | 38 | 97.4359 | |
| asubramanian-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0572 | 98.8725 | 99.2426 | 41.5382 | 10611 | 121 | 10614 | 81 | 2 | 2.4691 | |
| mlin-fermikit | SNP | * | HG002compoundhet | homalt | 92.6523 | 98.4233 | 87.5206 | 41.6338 | 10612 | 170 | 10618 | 1514 | 1310 | 86.5258 | |
| anovak-vg | SNP | ti | map_l125_m0_e0 | * | 79.1475 | 83.1766 | 75.4908 | 80.4095 | 10615 | 2147 | 10537 | 3421 | 933 | 27.2727 | |
| ndellapenna-hhga | INDEL | I1_5 | * | hetalt | 97.0167 | 94.8280 | 99.3087 | 62.5367 | 10616 | 579 | 10630 | 74 | 67 | 90.5405 | |
| ndellapenna-hhga | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.2708 | 98.9378 | 99.6061 | 37.1789 | 10618 | 114 | 10620 | 42 | 29 | 69.0476 | |
| gduggal-bwafb | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.4458 | 98.9378 | 97.9586 | 49.7551 | 10618 | 114 | 10653 | 222 | 58 | 26.1261 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 71.6758 | 63.5678 | 82.1546 | 59.3969 | 10619 | 6086 | 3241 | 704 | 487 | 69.1761 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 71.6758 | 63.5678 | 82.1546 | 59.3969 | 10619 | 6086 | 3241 | 704 | 487 | 69.1761 | |
| ckim-isaac | SNP | * | map_l125_m0_e0 | * | 70.7547 | 54.8207 | 99.7466 | 75.5092 | 10627 | 8758 | 10627 | 27 | 5 | 18.5185 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.6358 | 95.7046 | 99.6464 | 30.5076 | 10628 | 477 | 10709 | 38 | 37 | 97.3684 | |
| jpowers-varprowl | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.3288 | 99.0403 | 97.6276 | 52.2232 | 10629 | 103 | 10658 | 259 | 68 | 26.2548 | |
| egarrison-hhga | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3832 | 99.0868 | 99.6813 | 36.6712 | 10634 | 98 | 10635 | 34 | 19 | 55.8824 | |
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.1238 | 98.4538 | 99.8029 | 79.4946 | 10634 | 167 | 10634 | 21 | 12 | 57.1429 | |
| ltrigg-rtg2 | SNP | tv | map_l150_m1_e0 | * | 98.6367 | 97.4707 | 99.8310 | 62.1132 | 10636 | 276 | 10635 | 18 | 2 | 11.1111 | |
| astatham-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.5369 | 99.1334 | 99.9436 | 40.3106 | 10639 | 93 | 10639 | 6 | 1 | 16.6667 | |
| jmaeng-gatk | SNP | * | segdup | homalt | 99.4625 | 99.0412 | 99.8873 | 88.3992 | 10640 | 103 | 10640 | 12 | 12 | 100.0000 | |
| ckim-gatk | SNP | * | segdup | homalt | 99.4811 | 99.0505 | 99.9155 | 88.5459 | 10641 | 102 | 10641 | 9 | 9 | 100.0000 | |
| gduggal-snapplat | SNP | * | segdup | homalt | 99.4486 | 99.0692 | 99.8310 | 88.7280 | 10643 | 100 | 10636 | 18 | 13 | 72.2222 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 93.7133 | 98.5372 | 89.3396 | 84.5796 | 10643 | 158 | 9822 | 1172 | 111 | 9.4710 | |
| egarrison-hhga | INDEL | I1_5 | HG002compoundhet | hetalt | 97.3530 | 95.2492 | 99.5519 | 56.2316 | 10646 | 531 | 10663 | 48 | 44 | 91.6667 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 95.8320 | 92.1659 | 99.8018 | 61.7166 | 10647 | 905 | 10577 | 21 | 11 | 52.3810 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.8320 | 92.1659 | 99.8018 | 61.7166 | 10647 | 905 | 10577 | 21 | 11 | 52.3810 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.3372 | 98.5927 | 92.2897 | 84.7602 | 10649 | 152 | 10677 | 892 | 112 | 12.5561 | |
| qzeng-custom | SNP | * | segdup | homalt | 99.2653 | 99.1250 | 99.4061 | 87.8458 | 10649 | 94 | 10544 | 63 | 57 | 90.4762 | |
| hfeng-pmm1 | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.6121 | 99.2918 | 99.9344 | 37.2432 | 10656 | 76 | 10656 | 7 | 1 | 14.2857 | |
| hfeng-pmm2 | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.6074 | 99.3012 | 99.9156 | 37.6986 | 10657 | 75 | 10657 | 9 | 0 | 0.0000 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.7497 | 95.9658 | 99.6012 | 27.0945 | 10657 | 448 | 10739 | 43 | 42 | 97.6744 | |
| raldana-dualsentieon | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.5098 | 99.3105 | 99.7100 | 37.0828 | 10658 | 74 | 10658 | 31 | 2 | 6.4516 | |
| hfeng-pmm3 | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.6122 | 99.3198 | 99.9063 | 37.9962 | 10659 | 73 | 10659 | 10 | 4 | 40.0000 | |
| egarrison-hhga | INDEL | I1_5 | * | hetalt | 97.2375 | 95.2479 | 99.3119 | 61.7967 | 10663 | 532 | 10681 | 74 | 69 | 93.2432 | |
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3478 | 99.3571 | 99.3386 | 42.1628 | 10663 | 69 | 10663 | 71 | 1 | 1.4085 | |
| qzeng-custom | SNP | * | HG002compoundhet | homalt | 98.8868 | 98.8963 | 98.8772 | 42.3069 | 10663 | 119 | 8190 | 93 | 74 | 79.5699 | |
| ghariani-varprowl | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 96.7473 | 99.3571 | 94.2711 | 57.1736 | 10663 | 69 | 10696 | 650 | 69 | 10.6154 | |
| jpowers-varprowl | INDEL | D6_15 | * | het | 70.9404 | 91.9945 | 57.7285 | 54.4042 | 10664 | 928 | 10689 | 7827 | 7764 | 99.1951 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.5773 | 96.2462 | 96.9108 | 49.8130 | 10666 | 416 | 10666 | 340 | 299 | 87.9412 | |
| ltrigg-rtg2 | SNP | * | HG002compoundhet | homalt | 99.4265 | 98.9241 | 99.9340 | 32.8863 | 10666 | 116 | 10603 | 7 | 6 | 85.7143 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.5533 | 98.7871 | 98.3205 | 78.4263 | 10670 | 131 | 10713 | 183 | 3 | 1.6393 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.4310 | 98.7964 | 96.1027 | 79.7737 | 10671 | 130 | 10702 | 434 | 19 | 4.3779 | |