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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
3601-3650 / 86044 show all | |||||||||||||||
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 66.7282 | 78.5285 | 58.0110 | 55.6155 | 1046 | 286 | 1050 | 760 | 754 | 99.2105 | |
| ckim-dragen | SNP | * | map_l150_m1_e0 | * | 98.2024 | 98.8631 | 97.5505 | 76.7332 | 30261 | 348 | 30267 | 760 | 93 | 12.2368 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 40.9601 | 29.3830 | 67.5918 | 54.6739 | 1743 | 4189 | 1583 | 759 | 616 | 81.1594 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 57.5781 | 55.1232 | 60.2618 | 82.2738 | 850 | 692 | 1151 | 759 | 32 | 4.2161 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 93.2809 | 95.5574 | 91.1103 | 49.1422 | 8023 | 373 | 7779 | 759 | 657 | 86.5613 | |
| gduggal-bwavard | SNP | ti | map_l250_m1_e0 | het | 87.4417 | 97.6415 | 79.1712 | 92.9128 | 2898 | 70 | 2885 | 759 | 20 | 2.6351 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 43.8454 | 39.1619 | 49.8013 | 62.4191 | 757 | 1176 | 752 | 758 | 719 | 94.8549 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 86.7930 | 84.0381 | 89.7346 | 47.2948 | 2027 | 385 | 6626 | 758 | 648 | 85.4881 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 55.0422 | 49.2827 | 62.3260 | 55.4966 | 1168 | 1202 | 1254 | 758 | 535 | 70.5805 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.4429 | 96.9236 | 97.9678 | 56.0572 | 36736 | 1166 | 36542 | 758 | 728 | 96.0422 | |
| gduggal-snapvard | INDEL | C1_5 | HG002compoundhet | het | 0.0000 | 0.0000 | 29.6193 | 80.5174 | 0 | 0 | 319 | 758 | 106 | 13.9842 | |
| gduggal-bwafb | SNP | ti | map_siren | het | 99.0568 | 99.3219 | 98.7930 | 59.4400 | 61959 | 423 | 61963 | 757 | 131 | 17.3052 | |
| gduggal-bwafb | SNP | * | map_l100_m2_e0 | het | 98.6971 | 99.0172 | 98.3791 | 71.2956 | 45943 | 456 | 45945 | 757 | 143 | 18.8904 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 18.7853 | 15.3926 | 24.0964 | 85.0898 | 149 | 819 | 240 | 756 | 119 | 15.7407 | |
| qzeng-custom | SNP | ti | * | homalt | 99.6207 | 99.3383 | 99.9047 | 15.9860 | 797725 | 5314 | 792891 | 756 | 473 | 62.5661 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 96.6367 | 99.6517 | 93.7987 | 63.9277 | 11444 | 40 | 11435 | 756 | 746 | 98.6772 | |
| jpowers-varprowl | INDEL | D1_5 | * | homalt | 93.6510 | 89.4228 | 98.2990 | 49.9719 | 43751 | 5175 | 43688 | 756 | 634 | 83.8624 | |
| jmaeng-gatk | SNP | tv | map_siren | * | 92.8750 | 88.1232 | 98.1685 | 71.3358 | 40475 | 5455 | 40467 | 755 | 31 | 4.1060 | |
| mlin-fermikit | SNP | * | map_siren | het | 82.6394 | 70.9993 | 98.8447 | 48.1176 | 64603 | 26388 | 64595 | 755 | 18 | 2.3841 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 88.5028 | 99.3917 | 79.7641 | 72.5419 | 2941 | 18 | 2976 | 755 | 16 | 2.1192 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 62.1311 | 88.2872 | 47.9310 | 90.8828 | 701 | 93 | 695 | 755 | 39 | 5.1656 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 84.9840 | 84.8017 | 85.1670 | 81.2419 | 4341 | 778 | 4335 | 755 | 704 | 93.2450 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 52.0817 | 37.5305 | 85.0613 | 64.9709 | 4310 | 7174 | 4299 | 755 | 639 | 84.6358 | |
| eyeh-varpipe | SNP | * | map_l150_m1_e0 | * | 98.5692 | 99.6472 | 97.5143 | 77.5222 | 30501 | 108 | 29619 | 755 | 30 | 3.9735 | |
| ckim-gatk | SNP | * | map_l125_m1_e0 | * | 84.2159 | 73.9471 | 97.7967 | 84.1626 | 33518 | 11809 | 33512 | 755 | 58 | 7.6821 | |
| gduggal-snapplat | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 54.4770 | 39.2554 | 88.9798 | 82.4941 | 6052 | 9365 | 6088 | 754 | 644 | 85.4111 | |
| gduggal-snapplat | INDEL | I1_5 | * | hetalt | 55.9163 | 41.4113 | 86.0603 | 83.9805 | 4636 | 6559 | 4655 | 754 | 516 | 68.4350 | |
| gduggal-snapfb | SNP | tv | lowcmp_SimpleRepeat_diTR_51to200 | het | 3.0730 | 70.5882 | 1.5707 | 75.7691 | 12 | 5 | 12 | 752 | 2 | 0.2660 | |
| ghariani-varprowl | SNP | tv | map_l100_m1_e0 | het | 97.2713 | 99.3060 | 95.3184 | 75.1777 | 15310 | 107 | 15311 | 752 | 97 | 12.8989 | |
| qzeng-custom | SNP | * | map_l125_m2_e1 | het | 84.1292 | 74.4636 | 96.6784 | 86.6172 | 22071 | 7569 | 21888 | 752 | 615 | 81.7819 | |
| jpowers-varprowl | SNP | * | map_l100_m0_e0 | * | 97.2063 | 96.7297 | 97.6876 | 74.3551 | 31767 | 1074 | 31768 | 752 | 236 | 31.3830 | |
| eyeh-varpipe | SNP | tv | HG002complexvar | * | 99.7847 | 99.8883 | 99.6813 | 20.5762 | 245880 | 275 | 235205 | 752 | 120 | 15.9574 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 88.0775 | 95.1208 | 82.0053 | 38.4898 | 2047 | 105 | 3427 | 752 | 750 | 99.7340 | |
| egarrison-hhga | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.7893 | 98.0137 | 97.5659 | 71.4911 | 30150 | 611 | 30142 | 752 | 362 | 48.1383 | |
| qzeng-custom | SNP | * | map_l125_m2_e0 | het | 84.0186 | 74.3127 | 96.6407 | 86.6277 | 21787 | 7531 | 21605 | 751 | 614 | 81.7577 | |
| ckim-dragen | SNP | * | map_l150_m2_e0 | het | 97.5195 | 98.7086 | 96.3588 | 81.7586 | 19873 | 260 | 19874 | 751 | 69 | 9.1878 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.7491 | 97.4988 | 98.0006 | 56.6076 | 36954 | 948 | 36761 | 750 | 723 | 96.4000 | |
| ciseli-custom | SNP | tv | map_l125_m0_e0 | het | 70.2747 | 63.3947 | 78.8298 | 84.9536 | 2790 | 1611 | 2789 | 749 | 26 | 3.4713 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 96.8049 | 97.4163 | 96.2011 | 51.9614 | 10821 | 287 | 18967 | 749 | 273 | 36.4486 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.6451 | 97.4107 | 97.8807 | 69.5745 | 5944 | 158 | 34593 | 749 | 587 | 78.3712 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 69.3518 | 70.9929 | 67.7849 | 64.5633 | 1001 | 409 | 1576 | 749 | 136 | 18.1575 | |
| ckim-gatk | SNP | * | map_l125_m1_e0 | het | 88.2494 | 81.0510 | 96.8511 | 86.4318 | 23012 | 5380 | 23006 | 748 | 54 | 7.2193 | |
| hfeng-pmm3 | INDEL | * | HG002compoundhet | * | 94.8142 | 92.3999 | 97.3580 | 58.7757 | 27683 | 2277 | 27564 | 748 | 724 | 96.7914 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 50.9329 | 44.5458 | 59.4580 | 50.1890 | 1074 | 1337 | 1097 | 748 | 692 | 92.5134 | |
| jpowers-varprowl | SNP | * | map_l150_m2_e1 | * | 97.1814 | 96.7122 | 97.6551 | 80.7455 | 31151 | 1059 | 31151 | 748 | 233 | 31.1497 | |
| jmaeng-gatk | SNP | tv | map_siren | het | 94.8661 | 92.5932 | 97.2533 | 75.2567 | 26490 | 2119 | 26485 | 748 | 25 | 3.3423 | |
| jpowers-varprowl | SNP | * | HG002complexvar | het | 99.3948 | 98.9553 | 99.8382 | 20.0313 | 460632 | 4863 | 460862 | 747 | 150 | 20.0803 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 42.7693 | 45.3355 | 40.4781 | 43.2897 | 277 | 334 | 508 | 747 | 649 | 86.8809 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.8256 | 97.5251 | 96.1361 | 70.1065 | 17378 | 441 | 18561 | 746 | 415 | 55.6300 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 97.1108 | 97.1608 | 97.0609 | 55.5769 | 24639 | 720 | 24636 | 746 | 544 | 72.9223 | |