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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
2751-2800 / 86044 show all | |||||||||||||||
| gduggal-snapplat | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 77.1866 | 71.6422 | 83.6612 | 80.1878 | 23811 | 9425 | 27896 | 5448 | 1746 | 32.0485 | |
| gduggal-snapfb | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 91.4953 | 90.7025 | 92.3021 | 74.5517 | 27901 | 2860 | 27890 | 2326 | 2006 | 86.2425 | |
| ckim-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.6801 | 99.7532 | 99.6071 | 56.0538 | 27890 | 69 | 27889 | 110 | 11 | 10.0000 | |
| jmaeng-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.7157 | 99.7174 | 99.7139 | 56.2929 | 27880 | 79 | 27879 | 80 | 10 | 12.5000 | |
| ckim-gatk | SNP | * | segdup | * | 98.8880 | 99.3409 | 98.4392 | 93.5811 | 27882 | 185 | 27876 | 442 | 14 | 3.1674 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4714 | 99.5136 | 99.4293 | 48.5634 | 27823 | 136 | 27875 | 160 | 12 | 7.5000 | |
| ciseli-custom | INDEL | I1_5 | HG002complexvar | * | 86.2012 | 84.5873 | 87.8779 | 52.9140 | 28220 | 5142 | 27874 | 3845 | 2974 | 77.3472 | |
| ckim-dragen | INDEL | * | HG002compoundhet | * | 93.6532 | 93.4379 | 93.8696 | 62.4863 | 27994 | 1966 | 27868 | 1820 | 1806 | 99.2308 | |
| gduggal-bwavard | SNP | tv | map_siren | het | 95.7305 | 97.7804 | 93.7647 | 72.5806 | 27974 | 635 | 27865 | 1853 | 145 | 7.8252 | |
| jmaeng-gatk | SNP | * | segdup | * | 98.5236 | 99.2803 | 97.7783 | 93.6584 | 27865 | 202 | 27859 | 633 | 14 | 2.2117 | |
| jpowers-varprowl | SNP | * | segdup | * | 98.1671 | 99.2090 | 97.1467 | 91.9113 | 27845 | 222 | 27851 | 818 | 71 | 8.6797 | |
| asubramanian-gatk | INDEL | * | HG002compoundhet | * | 93.4362 | 93.2377 | 93.6356 | 65.8907 | 27934 | 2026 | 27836 | 1892 | 1575 | 83.2452 | |
| anovak-vg | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 95.7089 | 96.7345 | 94.7048 | 54.9593 | 27046 | 913 | 27829 | 1556 | 769 | 49.4216 | |
| ndellapenna-hhga | SNP | * | map_l125_m1_e0 | het | 98.8381 | 97.9748 | 99.7168 | 68.7996 | 27817 | 575 | 27817 | 79 | 36 | 45.5696 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.7858 | 98.2767 | 99.3002 | 57.2345 | 27773 | 487 | 27812 | 196 | 123 | 62.7551 | |
| gduggal-snapplat | SNP | * | map_l125_m2_e1 | het | 93.8837 | 93.6910 | 94.0772 | 85.0315 | 27770 | 1870 | 27797 | 1750 | 928 | 53.0286 | |
| ghariani-varprowl | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 95.1859 | 99.0236 | 91.6345 | 64.6332 | 27686 | 273 | 27790 | 2537 | 281 | 11.0761 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 72.8692 | 95.0543 | 59.0803 | 78.2168 | 27292 | 1420 | 27789 | 19247 | 483 | 2.5095 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 72.8692 | 95.0543 | 59.0803 | 78.2168 | 27292 | 1420 | 27789 | 19247 | 483 | 2.5095 | |
| anovak-vg | SNP | ti | map_l100_m2_e1 | het | 80.9356 | 90.4328 | 73.2435 | 73.3025 | 27998 | 2962 | 27782 | 10149 | 2220 | 21.8741 | |
| ckim-vqsr | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.5289 | 99.3598 | 99.6985 | 56.1737 | 27780 | 179 | 27779 | 84 | 9 | 10.7143 | |
| hfeng-pmm2 | SNP | * | map_l100_m2_e1 | homalt | 99.8687 | 99.8741 | 99.8633 | 63.3911 | 27761 | 35 | 27761 | 38 | 19 | 50.0000 | |
| rpoplin-dv42 | INDEL | * | HG002compoundhet | * | 93.3591 | 92.7336 | 93.9930 | 68.4001 | 27783 | 2177 | 27758 | 1774 | 1747 | 98.4780 | |
| gduggal-bwafb | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.2991 | 99.0593 | 97.5505 | 61.1472 | 27696 | 263 | 27758 | 697 | 164 | 23.5294 | |
| hfeng-pmm1 | SNP | * | map_l100_m2_e1 | homalt | 99.8597 | 99.8453 | 99.8740 | 63.3660 | 27753 | 43 | 27753 | 35 | 17 | 48.5714 | |
| hfeng-pmm3 | SNP | * | map_l100_m2_e1 | homalt | 99.8561 | 99.8381 | 99.8740 | 63.2761 | 27751 | 45 | 27751 | 35 | 17 | 48.5714 | |
| anovak-vg | SNP | * | map_l100_m0_e0 | * | 81.2078 | 85.4511 | 77.3660 | 74.7301 | 28063 | 4778 | 27745 | 8117 | 2172 | 26.7587 | |
| ltrigg-rtg1 | SNP | * | map_l125_m1_e0 | het | 98.7065 | 97.7001 | 99.7339 | 59.7345 | 27739 | 653 | 27739 | 74 | 12 | 16.2162 | |
| egarrison-hhga | SNP | * | map_l100_m2_e1 | homalt | 99.8506 | 99.7698 | 99.9315 | 63.4220 | 27732 | 64 | 27732 | 19 | 18 | 94.7368 | |
| ltrigg-rtg1 | SNP | * | map_l100_m2_e1 | homalt | 99.8200 | 99.7446 | 99.8955 | 62.4711 | 27725 | 71 | 27724 | 29 | 26 | 89.6552 | |
| gduggal-snapplat | SNP | * | segdup | * | 98.9750 | 98.7209 | 99.2304 | 93.4858 | 27708 | 359 | 27723 | 215 | 30 | 13.9535 | |
| raldana-dualsentieon | SNP | * | map_l100_m2_e1 | homalt | 99.8307 | 99.7302 | 99.9315 | 59.5367 | 27721 | 75 | 27721 | 19 | 15 | 78.9474 | |
| gduggal-snapvard | SNP | tv | map_siren | het | 94.6657 | 97.2841 | 92.1846 | 72.3745 | 27832 | 777 | 27719 | 2350 | 198 | 8.4255 | |
| jpowers-varprowl | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.7595 | 98.7696 | 96.7698 | 62.5065 | 27615 | 344 | 27711 | 925 | 281 | 30.3784 | |
| ltrigg-rtg2 | SNP | * | map_l100_m2_e1 | homalt | 99.8127 | 99.6906 | 99.9351 | 60.3846 | 27710 | 86 | 27708 | 18 | 16 | 88.8889 | |
| bgallagher-sentieon | SNP | * | map_l100_m2_e1 | homalt | 99.7911 | 99.6654 | 99.9170 | 60.2187 | 27703 | 93 | 27703 | 23 | 18 | 78.2609 | |
| astatham-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.5168 | 99.0808 | 99.9567 | 54.7993 | 27702 | 257 | 27701 | 12 | 5 | 41.6667 | |
| ndellapenna-hhga | SNP | * | map_l100_m2_e1 | homalt | 99.7857 | 99.6546 | 99.9170 | 62.4746 | 27700 | 96 | 27700 | 23 | 21 | 91.3043 | |
| jli-custom | SNP | * | map_l100_m2_e1 | homalt | 99.7946 | 99.6510 | 99.9387 | 59.6958 | 27699 | 97 | 27699 | 17 | 16 | 94.1176 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.4995 | 98.0432 | 98.9602 | 56.0148 | 27707 | 553 | 27695 | 291 | 283 | 97.2509 | |
| egarrison-hhga | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.3239 | 99.0379 | 99.6116 | 52.2441 | 27690 | 269 | 27695 | 108 | 53 | 49.0741 | |
| anovak-vg | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 79.2304 | 81.6976 | 76.9079 | 69.6191 | 25131 | 5630 | 27693 | 8315 | 7083 | 85.1834 | |
| ckim-gatk | INDEL | * | HG002compoundhet | * | 93.9895 | 92.8338 | 95.1743 | 62.6651 | 27813 | 2147 | 27690 | 1404 | 1391 | 99.0741 | |
| gduggal-snapfb | SNP | * | map_l125_m1_e0 | het | 96.3552 | 97.4817 | 95.2545 | 71.3326 | 27677 | 715 | 27680 | 1379 | 599 | 43.4373 | |
| asubramanian-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.2429 | 98.9091 | 99.5790 | 55.5792 | 27654 | 305 | 27674 | 117 | 13 | 11.1111 | |
| ckim-dragen | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.8358 | 99.8591 | 99.8124 | 64.8592 | 27639 | 39 | 27673 | 52 | 16 | 30.7692 | |
| ckim-vqsr | INDEL | * | HG002compoundhet | * | 93.9622 | 92.7503 | 95.2061 | 62.6940 | 27788 | 2172 | 27665 | 1393 | 1381 | 99.1385 | |
| hfeng-pmm3 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4357 | 98.9449 | 99.9314 | 53.1567 | 27664 | 295 | 27664 | 19 | 7 | 36.8421 | |
| astatham-gatk | SNP | * | segdup | * | 99.1969 | 98.5784 | 99.8232 | 90.3648 | 27668 | 399 | 27662 | 49 | 12 | 24.4898 | |
| dgrover-gatk | SNP | * | map_l100_m2_e1 | homalt | 99.7116 | 99.4999 | 99.9241 | 60.6444 | 27657 | 139 | 27657 | 21 | 16 | 76.1905 | |