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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
77751-77800 / 86044 show all | |||||||||||||||
| anovak-vg | SNP | ti | map_l250_m2_e1 | homalt | 85.1502 | 74.4357 | 99.4681 | 88.0298 | 1319 | 453 | 1309 | 7 | 5 | 71.4286 | |
| bgallagher-sentieon | SNP | * | map_siren | * | 99.5992 | 99.6902 | 99.5084 | 55.5562 | 145775 | 453 | 145752 | 720 | 102 | 14.1667 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 12.8457 | 8.1136 | 30.8219 | 63.7717 | 40 | 453 | 45 | 101 | 70 | 69.3069 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 64.9109 | 100.0000 | 838 | 453 | 0 | 0 | 0 | ||||
| ckim-isaac | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 90.3594 | 91.9064 | 88.8636 | 53.3705 | 5144 | 453 | 4684 | 587 | 468 | 79.7274 | |
| ckim-isaac | INDEL | * | map_l100_m1_e0 | homalt | 77.1685 | 63.0807 | 99.3582 | 75.2463 | 774 | 453 | 774 | 5 | 3 | 60.0000 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.2779 | 95.1269 | 99.5285 | 62.9323 | 8843 | 453 | 8865 | 42 | 42 | 100.0000 | |
| ciseli-custom | INDEL | * | map_l100_m2_e0 | homalt | 69.5990 | 63.9968 | 76.2760 | 85.5956 | 807 | 454 | 807 | 251 | 203 | 80.8765 | |
| ciseli-custom | INDEL | D1_5 | map_l100_m2_e1 | * | 79.9331 | 76.5859 | 83.5863 | 88.3030 | 1485 | 454 | 1487 | 292 | 143 | 48.9726 | |
| ckim-gatk | INDEL | D6_15 | HG002compoundhet | hetalt | 96.9335 | 94.4301 | 99.5733 | 24.1244 | 7697 | 454 | 7701 | 33 | 33 | 100.0000 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 24.8195 | 14.3396 | 92.2078 | 60.3093 | 76 | 454 | 71 | 6 | 5 | 83.3333 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.1903 | 92.5366 | 93.8532 | 64.0267 | 5629 | 454 | 5512 | 361 | 345 | 95.5679 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m2_e0 | het | 76.7082 | 63.8535 | 96.0432 | 76.9422 | 802 | 454 | 801 | 33 | 18 | 54.5455 | |
| gduggal-bwavard | INDEL | D16_PLUS | HG002complexvar | * | 75.2016 | 72.3676 | 78.2666 | 64.6225 | 1189 | 454 | 1192 | 331 | 268 | 80.9668 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1951 | 98.6340 | 99.7626 | 72.6726 | 32782 | 454 | 32775 | 78 | 58 | 74.3590 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.1075 | 96.6926 | 99.5645 | 63.4833 | 13302 | 455 | 13260 | 58 | 44 | 75.8621 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.1075 | 96.6926 | 99.5645 | 63.4833 | 13302 | 455 | 13260 | 58 | 44 | 75.8621 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.6815 | 93.6024 | 99.9702 | 26.8790 | 6657 | 455 | 6701 | 2 | 1 | 50.0000 | |
| asubramanian-gatk | INDEL | * | map_l100_m2_e1 | * | 92.1115 | 87.8860 | 96.7638 | 96.1058 | 3301 | 455 | 3319 | 111 | 17 | 15.3153 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.8615 | 94.3541 | 99.5059 | 29.2939 | 7604 | 455 | 7652 | 38 | 38 | 100.0000 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.8615 | 94.3541 | 99.5059 | 29.2939 | 7604 | 455 | 7652 | 38 | 38 | 100.0000 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.4805 | 97.1646 | 97.7985 | 57.9258 | 15592 | 455 | 15593 | 351 | 340 | 96.8661 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 90.5987 | 83.2905 | 99.3127 | 36.1667 | 2268 | 455 | 2312 | 16 | 16 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | HG002compoundhet | hetalt | 96.9271 | 94.4179 | 99.5733 | 24.1268 | 7696 | 455 | 7700 | 33 | 33 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.1679 | 96.6993 | 97.6410 | 51.8960 | 13330 | 455 | 13328 | 322 | 315 | 97.8261 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.5627 | 95.6563 | 99.5467 | 33.3070 | 10020 | 455 | 10102 | 46 | 45 | 97.8261 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 48.9137 | 52.6535 | 45.6699 | 40.6819 | 506 | 455 | 1176 | 1399 | 1152 | 82.3445 | |
| gduggal-bwafb | INDEL | D16_PLUS | HG002compoundhet | hetalt | 86.2756 | 76.4004 | 99.0826 | 35.1190 | 1473 | 455 | 216 | 2 | 2 | 100.0000 | |
| qzeng-custom | INDEL | * | map_l100_m1_e0 | het | 83.3456 | 79.6421 | 87.4105 | 89.3842 | 1780 | 455 | 2319 | 334 | 53 | 15.8683 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m2_e1 | het | 76.7833 | 64.0379 | 95.8629 | 77.1351 | 812 | 456 | 811 | 35 | 19 | 54.2857 | |
| ckim-isaac | INDEL | D16_PLUS | HG002compoundhet | hetalt | 86.1574 | 76.3485 | 98.8582 | 24.5694 | 1472 | 456 | 1645 | 19 | 17 | 89.4737 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.8550 | 94.3417 | 99.5058 | 29.2966 | 7603 | 456 | 7651 | 38 | 38 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.8550 | 94.3417 | 99.5058 | 29.2966 | 7603 | 456 | 7651 | 38 | 38 | 100.0000 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.3304 | 96.9158 | 97.7485 | 53.9045 | 14329 | 456 | 14327 | 330 | 320 | 96.9697 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 49.6401 | 47.9452 | 51.4593 | 46.5298 | 420 | 456 | 670 | 632 | 480 | 75.9494 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 93.8831 | 89.7436 | 98.4229 | 41.9180 | 3990 | 456 | 10235 | 164 | 145 | 88.4146 | |
| gduggal-bwafb | SNP | * | map_l100_m2_e0 | het | 98.6971 | 99.0172 | 98.3791 | 71.2956 | 45943 | 456 | 45945 | 757 | 143 | 18.8904 | |
| gduggal-bwafb | SNP | * | map_l100_m2_e1 | het | 98.7046 | 99.0277 | 98.3837 | 71.3332 | 46442 | 456 | 46444 | 763 | 144 | 18.8729 | |
| gduggal-bwavard | INDEL | I16_PLUS | * | homalt | 81.4493 | 70.7880 | 95.8916 | 51.4843 | 1105 | 456 | 1097 | 47 | 14 | 29.7872 | |
| gduggal-bwaplat | INDEL | I1_5 | map_l100_m2_e0 | * | 79.7551 | 66.6667 | 99.2383 | 92.3930 | 912 | 456 | 912 | 7 | 2 | 28.5714 | |
| gduggal-bwaplat | SNP | * | map_l250_m0_e0 | homalt | 43.1421 | 27.5040 | 100.0000 | 97.6903 | 173 | 456 | 173 | 0 | 0 | ||
| gduggal-snapvard | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 28.7500 | 0.0000 | 0.0000 | 184 | 456 | 0 | 0 | 0 | ||
| gduggal-snapplat | SNP | ti | map_l250_m2_e0 | het | 88.7434 | 85.9865 | 91.6830 | 94.7245 | 2798 | 456 | 2800 | 254 | 132 | 51.9685 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 84.6909 | 92.5107 | 78.0901 | 74.9769 | 5645 | 457 | 32751 | 9189 | 7904 | 86.0159 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 84.7851 | 78.2485 | 92.5134 | 54.4520 | 1644 | 457 | 1557 | 126 | 122 | 96.8254 | |
| mlin-fermikit | SNP | tv | map_l250_m0_e0 | het | 33.2370 | 20.1049 | 95.8333 | 85.2399 | 115 | 457 | 115 | 5 | 0 | 0.0000 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 13.1543 | 7.1138 | 87.1795 | 80.6931 | 35 | 457 | 34 | 5 | 4 | 80.0000 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.4855 | 93.5742 | 99.5838 | 26.7211 | 6655 | 457 | 6699 | 28 | 28 | 100.0000 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 21.4797 | 14.7388 | 39.5833 | 70.4160 | 79 | 457 | 76 | 116 | 116 | 100.0000 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.4961 | 97.7763 | 99.2266 | 43.2593 | 20138 | 458 | 20142 | 157 | 149 | 94.9045 | |