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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
7101-7150 / 86044 show all | |||||||||||||||
| ckim-dragen | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 93.2099 | 99.2021 | 87.9004 | 61.3834 | 746 | 6 | 741 | 102 | 102 | 100.0000 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.4083 | 95.5986 | 99.2879 | 34.0400 | 7059 | 325 | 15476 | 111 | 102 | 91.8919 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1330 | 98.7273 | 99.5420 | 75.3696 | 32813 | 423 | 32819 | 151 | 102 | 67.5497 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 94.0166 | 98.1818 | 90.1905 | 68.4305 | 810 | 15 | 947 | 103 | 102 | 99.0291 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 94.0166 | 98.1818 | 90.1905 | 68.4305 | 810 | 15 | 947 | 103 | 102 | 99.0291 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.7407 | 99.3048 | 96.2251 | 62.9649 | 2714 | 19 | 2702 | 106 | 102 | 96.2264 | |
| bgallagher-sentieon | SNP | * | map_siren | * | 99.5992 | 99.6902 | 99.5084 | 55.5562 | 145775 | 453 | 145752 | 720 | 102 | 14.1667 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.2962 | 93.5743 | 97.0826 | 62.0727 | 3728 | 256 | 3727 | 112 | 102 | 91.0714 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 69.6845 | 73.4336 | 66.2996 | 51.5475 | 293 | 106 | 301 | 153 | 102 | 66.6667 | |
| anovak-vg | INDEL | * | map_l125_m0_e0 | homalt | 73.9644 | 80.6338 | 68.3140 | 87.4544 | 229 | 55 | 235 | 109 | 101 | 92.6606 | |
| anovak-vg | INDEL | * | map_l125_m2_e1 | het | 70.9268 | 68.8210 | 73.1655 | 89.5197 | 969 | 439 | 1017 | 373 | 101 | 27.0777 | |
| astatham-gatk | SNP | ti | * | * | 99.6161 | 99.2515 | 99.9833 | 17.5605 | 2069900 | 15611 | 2069836 | 345 | 101 | 29.2754 | |
| asubramanian-gatk | INDEL | * | HG002complexvar | homalt | 99.4823 | 99.5116 | 99.4530 | 57.3903 | 26895 | 132 | 26910 | 148 | 101 | 68.2432 | |
| rpoplin-dv42 | SNP | * | HG002complexvar | het | 99.8978 | 99.8245 | 99.9712 | 18.3215 | 464680 | 817 | 464534 | 134 | 101 | 75.3731 | |
| rpoplin-dv42 | SNP | * | map_l150_m0_e0 | * | 98.4495 | 98.1632 | 98.7374 | 78.1997 | 11811 | 221 | 11808 | 151 | 101 | 66.8874 | |
| rpoplin-dv42 | SNP | ti | map_l125_m1_e0 | * | 99.2894 | 99.0830 | 99.4967 | 68.8733 | 29066 | 269 | 29062 | 147 | 101 | 68.7075 | |
| raldana-dualsentieon | INDEL | D16_PLUS | * | * | 97.3178 | 96.6244 | 98.0213 | 67.0307 | 6555 | 229 | 6539 | 132 | 101 | 76.5152 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.5003 | 95.5391 | 97.4811 | 71.7827 | 4776 | 223 | 4760 | 123 | 101 | 82.1138 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.5003 | 95.5391 | 97.4811 | 71.7827 | 4776 | 223 | 4760 | 123 | 101 | 82.1138 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 56.2841 | 56.5217 | 56.0484 | 43.7642 | 130 | 100 | 139 | 109 | 101 | 92.6606 | |
| eyeh-varpipe | INDEL | D1_5 | HG002complexvar | hetalt | 66.7172 | 51.5533 | 94.5191 | 75.2098 | 697 | 655 | 1759 | 102 | 101 | 99.0196 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 92.9382 | 92.2964 | 93.5890 | 71.7186 | 1258 | 105 | 1708 | 117 | 101 | 86.3248 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 92.0166 | 86.7307 | 97.9886 | 88.3681 | 16981 | 2598 | 17002 | 349 | 101 | 28.9398 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 92.0166 | 86.7307 | 97.9886 | 88.3681 | 16981 | 2598 | 17002 | 349 | 101 | 28.9398 | |
| gduggal-bwafb | INDEL | D6_15 | HG002complexvar | homalt | 93.8652 | 96.3216 | 91.5309 | 60.1040 | 1126 | 43 | 1124 | 104 | 101 | 97.1154 | |
| gduggal-bwaplat | INDEL | D1_5 | HG002complexvar | het | 91.4572 | 85.1047 | 98.8344 | 59.4901 | 17672 | 3093 | 17637 | 208 | 101 | 48.5577 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 89.2536 | 84.1610 | 95.0022 | 64.8333 | 2237 | 421 | 2205 | 116 | 101 | 87.0690 | |
| gduggal-bwavard | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 93.4478 | 94.6950 | 92.2330 | 77.5820 | 2981 | 167 | 2945 | 248 | 101 | 40.7258 | |
| gduggal-bwavard | SNP | tv | map_l100_m2_e1 | * | 95.9192 | 97.7930 | 94.1158 | 76.6728 | 24725 | 558 | 24632 | 1540 | 101 | 6.5584 | |
| eyeh-varpipe | SNP | ti | HG002compoundhet | * | 97.7572 | 99.1589 | 96.3946 | 39.7398 | 17331 | 147 | 12860 | 481 | 101 | 20.9979 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 80.9804 | 74.1455 | 89.2034 | 78.7338 | 846 | 295 | 851 | 103 | 101 | 98.0583 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.2575 | 98.7987 | 99.7206 | 70.8721 | 63657 | 774 | 63532 | 178 | 101 | 56.7416 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 96.6400 | 96.0539 | 97.2332 | 85.1791 | 4917 | 202 | 4920 | 140 | 101 | 72.1429 | |
| qzeng-custom | SNP | tv | HG002complexvar | het | 99.0228 | 98.2997 | 99.7567 | 23.1864 | 148171 | 2563 | 146790 | 358 | 101 | 28.2123 | |
| 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 | |
| hfeng-pmm1 | INDEL | D1_5 | HG002compoundhet | * | 95.7858 | 92.7013 | 99.0826 | 62.4019 | 11342 | 893 | 11341 | 105 | 101 | 96.1905 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.3106 | 99.8446 | 98.7824 | 50.8940 | 8353 | 13 | 8356 | 103 | 101 | 98.0583 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.6132 | 95.1837 | 98.0864 | 57.9273 | 8004 | 405 | 7996 | 156 | 101 | 64.7436 | |
| ckim-vqsr | SNP | * | * | het | 99.4736 | 99.0611 | 99.8894 | 26.9578 | 1855996 | 17591 | 1855876 | 2054 | 101 | 4.9172 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 75.9388 | 61.7232 | 98.6618 | 39.1505 | 8661 | 5371 | 8184 | 111 | 101 | 90.9910 | |
| ckim-gatk | SNP | * | HG002complexvar | * | 99.5695 | 99.1746 | 99.9675 | 19.4723 | 748154 | 6227 | 748002 | 243 | 101 | 41.5638 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 91.2469 | 84.8746 | 98.6537 | 45.5252 | 9747 | 1737 | 9746 | 133 | 101 | 75.9398 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.4189 | 94.5959 | 94.2426 | 73.7195 | 2013 | 115 | 1997 | 122 | 101 | 82.7869 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 59.7519 | 97.7584 | 43.0248 | 79.6303 | 4143 | 95 | 4253 | 5632 | 101 | 1.7933 | |
| gduggal-snapplat | INDEL | I6_15 | HG002complexvar | homalt | 34.0455 | 24.6293 | 55.1181 | 60.1881 | 299 | 915 | 280 | 228 | 101 | 44.2982 | |
| gduggal-snapvard | SNP | * | map_l250_m2_e0 | * | 86.3034 | 95.4344 | 78.7671 | 91.5243 | 7525 | 360 | 7449 | 2008 | 101 | 5.0299 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 84.1610 | 92.6630 | 77.0880 | 87.8937 | 1023 | 81 | 1043 | 310 | 101 | 32.5806 | |
| jmaeng-gatk | SNP | * | map_siren | het | 95.7096 | 93.4477 | 98.0837 | 71.4678 | 85029 | 5962 | 85015 | 1661 | 101 | 6.0807 | |
| jli-custom | SNP | * | map_siren | * | 99.6458 | 99.5726 | 99.7192 | 52.4710 | 145603 | 625 | 145591 | 410 | 101 | 24.6341 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5033 | 98.1180 | 98.8917 | 42.6441 | 9280 | 178 | 9280 | 104 | 101 | 97.1154 | |