PrecisionFDA
Truth Challenge
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Explore HG002 comparison results
Use this interactive explorer to filter all results across submission entries and multiple dimensions.
| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
301-350 / 86044 show all | |||||||||||||||
| anovak-vg | SNP | tv | * | * | 98.3366 | 98.3717 | 98.3016 | 24.5602 | 953908 | 15790 | 951566 | 16441 | 6526 | 39.6934 | |
| asubramanian-gatk | SNP | ti | map_l100_m1_e0 | het | 64.3552 | 47.4851 | 99.8174 | 85.5215 | 14218 | 15724 | 14214 | 26 | 10 | 38.4615 | |
| ckim-vqsr | SNP | * | map_siren | het | 90.3081 | 82.7379 | 99.4031 | 73.7019 | 75284 | 15707 | 75273 | 452 | 26 | 5.7522 | |
| ckim-vqsr | SNP | * | map_l100_m1_e0 | homalt | 59.0007 | 41.8509 | 99.9646 | 77.1745 | 11301 | 15702 | 11301 | 4 | 3 | 75.0000 | |
| qzeng-custom | SNP | ti | * | * | 99.5194 | 99.2515 | 99.7887 | 20.8361 | 2069907 | 15611 | 2063126 | 4368 | 997 | 22.8251 | |
| astatham-gatk | SNP | ti | * | * | 99.6161 | 99.2515 | 99.9833 | 17.5605 | 2069900 | 15611 | 2069836 | 345 | 101 | 29.2754 | |
| gduggal-bwavard | INDEL | D1_5 | * | * | 90.6910 | 89.3918 | 92.0286 | 58.1851 | 131178 | 15567 | 129649 | 11230 | 9891 | 88.0766 | |
| ckim-vqsr | SNP | * | map_l150_m1_e0 | * | 65.6433 | 49.1783 | 98.6821 | 91.1099 | 15053 | 15556 | 15050 | 201 | 2 | 0.9950 | |
| gduggal-bwaplat | SNP | * | HG002complexvar | het | 97.5069 | 96.6621 | 98.3666 | 21.6545 | 449959 | 15538 | 450835 | 7486 | 872 | 11.6484 | |
| gduggal-bwafb | INDEL | * | * | * | 96.9474 | 95.5004 | 98.4390 | 56.3888 | 329039 | 15503 | 342492 | 5431 | 4691 | 86.3745 | |
| asubramanian-gatk | SNP | ti | map_l150_m2_e1 | * | 40.9816 | 25.7878 | 99.7572 | 94.2645 | 5344 | 15379 | 5342 | 13 | 5 | 38.4615 | |
| gduggal-snapfb | INDEL | * | * | het | 92.8434 | 92.0858 | 93.6136 | 55.1298 | 178769 | 15364 | 200114 | 13652 | 5023 | 36.7931 | |
| gduggal-bwavard | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 0.4605 | 0.0000 | 0.0000 | 71 | 15346 | 0 | 0 | 0 | ||
| gduggal-bwavard | INDEL | * | * | homalt | 93.4187 | 87.7664 | 99.8491 | 40.7725 | 109859 | 15313 | 109214 | 165 | 92 | 55.7576 | |
| jpowers-varprowl | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 0.9081 | 0.0000 | 0.0000 | 140 | 15277 | 0 | 0 | 0 | ||
| astatham-gatk | SNP | ti | * | het | 99.3889 | 98.8086 | 99.9762 | 18.5890 | 1266618 | 15273 | 1266563 | 302 | 60 | 19.8675 | |
| ghariani-varprowl | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 1.0638 | 0.0000 | 0.0000 | 164 | 15253 | 0 | 0 | 0 | ||
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 59.5761 | 58.3242 | 60.8829 | 60.3781 | 21342 | 15250 | 21309 | 13691 | 13201 | 96.4210 | |
| qzeng-custom | SNP | * | map_l100_m2_e1 | * | 87.9879 | 79.6031 | 98.3471 | 77.0361 | 59493 | 15244 | 58784 | 988 | 790 | 79.9595 | |
| asubramanian-gatk | SNP | ti | map_l150_m2_e0 | * | 40.8545 | 25.6874 | 99.7538 | 94.2642 | 5269 | 15243 | 5267 | 13 | 5 | 38.4615 | |
| anovak-vg | INDEL | I6_15 | * | * | 44.4248 | 38.7222 | 52.0973 | 38.6048 | 9612 | 15211 | 9514 | 8748 | 6474 | 74.0055 | |
| ckim-isaac | SNP | ti | HG002complexvar | homalt | 95.8992 | 92.1386 | 99.9798 | 16.1839 | 178255 | 15209 | 178286 | 36 | 29 | 80.5556 | |
| asubramanian-gatk | SNP | * | map_l125_m0_e0 | * | 35.5829 | 21.6508 | 99.8098 | 95.1193 | 4197 | 15188 | 4197 | 8 | 5 | 62.5000 | |
| qzeng-custom | SNP | * | map_l100_m2_e0 | * | 87.8989 | 79.4670 | 98.3325 | 77.0630 | 58777 | 15187 | 58084 | 985 | 789 | 80.1015 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 56.4553 | 51.6684 | 62.2197 | 60.5704 | 16228 | 15180 | 16207 | 9841 | 9672 | 98.2827 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 56.4553 | 51.6684 | 62.2197 | 60.5704 | 16228 | 15180 | 16207 | 9841 | 9672 | 98.2827 | |
| qzeng-custom | SNP | * | * | het | 99.4239 | 99.1899 | 99.6590 | 25.4299 | 1858423 | 15178 | 1850061 | 6331 | 818 | 12.9205 | |
| mlin-fermikit | SNP | ti | map_l125_m2_e1 | * | 64.3036 | 50.3876 | 88.8389 | 61.3583 | 15403 | 15166 | 15402 | 1935 | 1705 | 88.1137 | |
| qzeng-custom | SNP | * | map_l100_m1_e0 | * | 87.6931 | 79.1127 | 98.3611 | 75.8509 | 57280 | 15123 | 56597 | 943 | 784 | 83.1389 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 59.2431 | 51.8849 | 69.0334 | 76.6255 | 16296 | 15112 | 21147 | 9486 | 4195 | 44.2231 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 59.2431 | 51.8849 | 69.0334 | 76.6255 | 16296 | 15112 | 21147 | 9486 | 4195 | 44.2231 | |
| asubramanian-gatk | SNP | ti | map_l100_m0_e0 | * | 46.8392 | 30.5957 | 99.8501 | 90.3797 | 6661 | 15110 | 6661 | 10 | 5 | 50.0000 | |
| ckim-vqsr | SNP | tv | * | * | 99.1585 | 98.4420 | 99.8855 | 27.4583 | 954582 | 15108 | 954496 | 1094 | 57 | 5.2102 | |
| mlin-fermikit | SNP | ti | map_l125_m2_e0 | * | 64.0610 | 50.1091 | 88.7802 | 61.1948 | 15162 | 15096 | 15161 | 1916 | 1690 | 88.2046 | |
| ciseli-custom | INDEL | * | HG002complexvar | * | 81.0665 | 80.3871 | 81.7575 | 57.5412 | 61845 | 15089 | 61574 | 13739 | 8055 | 58.6287 | |
| gduggal-snapplat | SNP | ti | * | het | 98.9857 | 98.8246 | 99.1474 | 28.1840 | 1266829 | 15068 | 1267456 | 10899 | 1576 | 14.4600 | |
| gduggal-bwaplat | SNP | ti | HG002complexvar | * | 97.9838 | 97.0464 | 98.9394 | 19.5056 | 493419 | 15017 | 493754 | 5293 | 700 | 13.2250 | |
| gduggal-bwaplat | SNP | * | map_l150_m2_e1 | * | 69.5020 | 53.4244 | 99.4224 | 91.0196 | 17208 | 15002 | 17212 | 100 | 30 | 30.0000 | |
| ckim-vqsr | SNP | * | map_l100_m0_e0 | * | 70.1414 | 54.3558 | 98.8482 | 87.4638 | 17851 | 14990 | 17850 | 208 | 2 | 0.9615 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 60.8792 | 59.0648 | 62.8085 | 52.6630 | 21613 | 14979 | 21581 | 12779 | 12331 | 96.4942 | |
| asubramanian-gatk | SNP | ti | map_siren | homalt | 75.4177 | 60.5364 | 100.0000 | 61.0156 | 22953 | 14963 | 22947 | 0 | 0 | ||
| jmaeng-gatk | SNP | * | map_siren | * | 94.0415 | 89.7742 | 98.7347 | 67.2383 | 131275 | 14953 | 131252 | 1682 | 121 | 7.1938 | |
| mlin-fermikit | SNP | ti | map_l125_m1_e0 | * | 63.1485 | 49.0745 | 88.5410 | 56.6927 | 14396 | 14939 | 14395 | 1863 | 1654 | 88.7815 | |
| asubramanian-gatk | SNP | * | HG002complexvar | het | 98.3318 | 96.7914 | 99.9221 | 19.0611 | 450561 | 14936 | 450442 | 351 | 31 | 8.8319 | |
| ckim-vqsr | SNP | ti | * | homalt | 99.0608 | 98.1423 | 99.9967 | 16.3042 | 788120 | 14918 | 788111 | 26 | 25 | 96.1538 | |
| ckim-gatk | SNP | * | map_siren | * | 94.1020 | 89.7981 | 98.8391 | 66.9681 | 131310 | 14918 | 131287 | 1542 | 125 | 8.1064 | |
| asubramanian-gatk | SNP | ti | map_l150_m1_e0 | * | 39.2304 | 24.4115 | 99.8340 | 94.1489 | 4812 | 14900 | 4810 | 8 | 4 | 50.0000 | |
| gduggal-bwaplat | SNP | * | map_l150_m2_e0 | * | 69.3373 | 53.2274 | 99.4313 | 91.0275 | 16954 | 14898 | 16958 | 97 | 30 | 30.9278 | |
| asubramanian-gatk | SNP | tv | map_l100_m2_e1 | * | 58.2603 | 41.1264 | 99.8655 | 87.2297 | 10398 | 14885 | 10396 | 14 | 2 | 14.2857 | |
| gduggal-snapplat | INDEL | D1_5 | * | het | 85.0942 | 83.0201 | 87.2745 | 66.1285 | 72704 | 14870 | 86462 | 12607 | 2010 | 15.9435 | |