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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
79201-79250 / 86044 show all | |||||||||||||||
| jli-custom | INDEL | D1_5 | HG002complexvar | homalt | 99.9010 | 99.9151 | 99.8868 | 59.4114 | 10589 | 9 | 10593 | 12 | 10 | 83.3333 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 55.8462 | 84.1067 | 41.8008 | 48.8238 | 10531 | 1990 | 10594 | 14750 | 14683 | 99.5458 | |
| raldana-dualsentieon | INDEL | D1_5 | HG002complexvar | homalt | 99.8492 | 99.9151 | 99.7834 | 59.8813 | 10589 | 9 | 10594 | 23 | 21 | 91.3043 | |
| bgallagher-sentieon | INDEL | D1_5 | HG002complexvar | homalt | 99.8445 | 99.9151 | 99.7740 | 60.1815 | 10589 | 9 | 10594 | 24 | 22 | 91.6667 | |
| astatham-gatk | SNP | * | map_l150_m0_e0 | * | 93.4108 | 88.0735 | 99.4368 | 82.7630 | 10597 | 1435 | 10594 | 60 | 21 | 35.0000 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.4707 | 98.0557 | 98.8892 | 80.4368 | 10591 | 210 | 10594 | 119 | 52 | 43.6975 | |
| dgrover-gatk | INDEL | D1_5 | HG002complexvar | homalt | 99.8963 | 99.9245 | 99.8680 | 60.1555 | 10590 | 8 | 10595 | 14 | 12 | 85.7143 | |
| mlin-fermikit | SNP | * | segdup | homalt | 98.6182 | 98.6689 | 98.5676 | 86.0366 | 10600 | 143 | 10597 | 154 | 135 | 87.6623 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.2978 | 94.0048 | 98.7055 | 32.8581 | 9847 | 628 | 10599 | 139 | 132 | 94.9640 | |
| ltrigg-rtg2 | SNP | * | HG002compoundhet | homalt | 99.4265 | 98.9241 | 99.9340 | 32.8863 | 10666 | 116 | 10603 | 7 | 6 | 85.7143 | |
| ciseli-custom | SNP | * | segdup | homalt | 98.3606 | 99.4694 | 97.2762 | 88.7149 | 10686 | 57 | 10607 | 297 | 168 | 56.5657 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.6965 | 98.0478 | 99.3539 | 59.8156 | 10698 | 213 | 10610 | 69 | 47 | 68.1159 | |
| ndellapenna-hhga | INDEL | I1_5 | HG002compoundhet | hetalt | 97.1229 | 94.8287 | 99.5310 | 57.0294 | 10599 | 578 | 10611 | 50 | 44 | 88.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | HG002compoundhet | hetalt | 97.1381 | 94.4439 | 99.9906 | 55.8738 | 10556 | 621 | 10614 | 1 | 1 | 100.0000 | |
| 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 | |
| hfeng-pmm1 | INDEL | I1_5 | HG002compoundhet | hetalt | 97.1665 | 94.4976 | 99.9906 | 57.5817 | 10562 | 615 | 10618 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.2708 | 98.9378 | 99.6061 | 37.1789 | 10618 | 114 | 10620 | 42 | 29 | 69.0476 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.5877 | 98.1945 | 98.9841 | 59.2905 | 10714 | 197 | 10620 | 109 | 34 | 31.1927 | |
| astatham-gatk | INDEL | I1_5 | HG002compoundhet | hetalt | 97.1718 | 94.5245 | 99.9718 | 56.8751 | 10565 | 612 | 10626 | 3 | 3 | 100.0000 | |
| gduggal-snapvard | SNP | * | map_l150_m1_e0 | homalt | 97.6436 | 95.6533 | 99.7185 | 71.0895 | 10783 | 490 | 10627 | 30 | 24 | 80.0000 | |
| ckim-isaac | SNP | * | map_l125_m0_e0 | * | 70.7547 | 54.8207 | 99.7466 | 75.5092 | 10627 | 8758 | 10627 | 27 | 5 | 18.5185 | |
| gduggal-bwavard | SNP | ti | map_l125_m1_e0 | homalt | 98.6148 | 97.3744 | 99.8872 | 66.1535 | 10755 | 290 | 10628 | 12 | 9 | 75.0000 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 71.3041 | 72.8754 | 69.7991 | 45.2762 | 8095 | 3013 | 10629 | 4599 | 3296 | 71.6678 | |
| ndellapenna-hhga | INDEL | I1_5 | * | hetalt | 97.0167 | 94.8280 | 99.3087 | 62.5367 | 10616 | 579 | 10630 | 74 | 67 | 90.5405 | |
| hfeng-pmm3 | INDEL | I1_5 | * | hetalt | 97.1290 | 94.4350 | 99.9812 | 61.2138 | 10572 | 623 | 10632 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.4426 | 95.0383 | 99.9718 | 29.9341 | 10554 | 551 | 10633 | 3 | 2 | 66.6667 | |
| 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 | |
| egarrison-hhga | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3832 | 99.0868 | 99.6813 | 36.6712 | 10634 | 98 | 10635 | 34 | 19 | 55.8824 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.1813 | 97.7317 | 92.7606 | 85.9802 | 10556 | 245 | 10635 | 830 | 248 | 29.8795 | |
| ltrigg-rtg2 | SNP | tv | map_l150_m1_e0 | * | 98.6367 | 97.4707 | 99.8310 | 62.1132 | 10636 | 276 | 10635 | 18 | 2 | 11.1111 | |
| gduggal-snapplat | SNP | * | segdup | homalt | 99.4486 | 99.0692 | 99.8310 | 88.7280 | 10643 | 100 | 10636 | 18 | 13 | 72.2222 | |
| hfeng-pmm1 | INDEL | I1_5 | * | hetalt | 97.1621 | 94.4975 | 99.9812 | 62.7564 | 10579 | 616 | 10637 | 2 | 2 | 100.0000 | |
| 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 | |
| hfeng-pmm2 | INDEL | I1_5 | HG002compoundhet | hetalt | 97.2799 | 94.7124 | 99.9906 | 57.4359 | 10586 | 591 | 10643 | 1 | 1 | 100.0000 | |
| astatham-gatk | INDEL | I1_5 | * | hetalt | 97.1674 | 94.5243 | 99.9624 | 62.1019 | 10582 | 613 | 10645 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | HG002compoundhet | hetalt | 97.2852 | 94.7392 | 99.9718 | 57.2014 | 10589 | 588 | 10650 | 3 | 3 | 100.0000 | |
| gduggal-bwafb | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.4458 | 98.9378 | 97.9586 | 49.7551 | 10618 | 114 | 10653 | 222 | 58 | 26.1261 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 87.7327 | 97.7687 | 79.5653 | 85.1430 | 10560 | 241 | 10653 | 2736 | 243 | 8.8816 | |
| 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 | |
| jpowers-varprowl | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.3288 | 99.0403 | 97.6276 | 52.2232 | 10629 | 103 | 10658 | 259 | 68 | 26.2548 | |
| 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 | |
| hfeng-pmm2 | INDEL | I1_5 | * | hetalt | 97.2753 | 94.7119 | 99.9812 | 62.6532 | 10603 | 592 | 10662 | 2 | 2 | 100.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3478 | 99.3571 | 99.3386 | 42.1628 | 10663 | 69 | 10663 | 71 | 1 | 1.4085 | |
| egarrison-hhga | INDEL | I1_5 | HG002compoundhet | hetalt | 97.3530 | 95.2492 | 99.5519 | 56.2316 | 10646 | 531 | 10663 | 48 | 44 | 91.6667 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.0481 | 94.6421 | 99.5798 | 42.9211 | 10510 | 595 | 10663 | 45 | 44 | 97.7778 | |