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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
7401-7450 / 86044 show all | |||||||||||||||
| jli-custom | SNP | ti | HG002compoundhet | het | 99.6793 | 99.7265 | 99.6321 | 39.4553 | 9479 | 26 | 9479 | 35 | 14 | 40.0000 | |
| jlack-gatk | SNP | ti | HG002compoundhet | het | 99.4749 | 99.6739 | 99.2768 | 41.5881 | 9474 | 31 | 9472 | 69 | 16 | 23.1884 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.1247 | 99.5589 | 96.7314 | 45.9773 | 9479 | 42 | 9470 | 320 | 309 | 96.5625 | |
| ckim-isaac | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 96.6931 | 93.6813 | 99.9050 | 54.1997 | 9459 | 638 | 9468 | 9 | 7 | 77.7778 | |
| gduggal-bwaplat | INDEL | D1_5 | HG002complexvar | homalt | 93.6134 | 89.6018 | 98.0010 | 59.6110 | 9496 | 1102 | 9462 | 193 | 170 | 88.0829 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.8573 | 92.4054 | 93.3136 | 74.7428 | 9308 | 765 | 9462 | 678 | 457 | 67.4041 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 75.4653 | 90.5356 | 64.6962 | 41.2162 | 1234 | 129 | 9456 | 5160 | 4823 | 93.4690 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 96.8247 | 99.2858 | 94.4828 | 49.5258 | 9453 | 68 | 9453 | 552 | 547 | 99.0942 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.9842 | 99.2753 | 98.6948 | 48.1764 | 9452 | 69 | 9452 | 125 | 120 | 96.0000 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.9583 | 99.2753 | 98.6433 | 48.3478 | 9452 | 69 | 9452 | 130 | 127 | 97.6923 | |
| gduggal-bwafb | SNP | ti | HG002compoundhet | het | 96.9467 | 98.6218 | 95.3275 | 45.8199 | 9374 | 131 | 9446 | 463 | 78 | 16.8467 | |
| rpoplin-dv42 | SNP | ti | HG002compoundhet | het | 99.5469 | 99.3898 | 99.7044 | 38.8720 | 9447 | 58 | 9445 | 28 | 22 | 78.5714 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.7555 | 99.1808 | 98.3339 | 49.8381 | 9443 | 78 | 9443 | 160 | 156 | 97.5000 | |
| gduggal-snapfb | SNP | ti | HG002compoundhet | het | 78.4798 | 97.2856 | 65.7667 | 46.9249 | 9247 | 258 | 9427 | 4907 | 174 | 3.5460 | |
| hfeng-pmm3 | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5415 | 97.2452 | 99.8728 | 66.2892 | 9425 | 267 | 9425 | 12 | 5 | 41.6667 | |
| raldana-dualsentieon | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5310 | 97.2348 | 99.8622 | 66.0735 | 9424 | 268 | 9424 | 13 | 11 | 84.6154 | |
| ckim-gatk | SNP | ti | HG002compoundhet | het | 99.4351 | 99.0847 | 99.7881 | 40.5181 | 9418 | 87 | 9418 | 20 | 15 | 75.0000 | |
| gduggal-snapplat | SNP | tv | map_l125_m1_e0 | het | 93.1767 | 92.9883 | 93.3657 | 84.9692 | 9416 | 710 | 9415 | 669 | 344 | 51.4200 | |
| hfeng-pmm1 | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.4982 | 97.1110 | 99.9257 | 65.7528 | 9412 | 280 | 9412 | 7 | 6 | 85.7143 | |
| eyeh-varpipe | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4099 | 99.4850 | 99.3350 | 55.8574 | 10045 | 52 | 9410 | 63 | 21 | 33.3333 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 93.3883 | 91.3830 | 95.4836 | 39.3587 | 8643 | 815 | 9408 | 445 | 428 | 96.1798 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.4377 | 98.0757 | 98.8024 | 44.1799 | 3211 | 63 | 9405 | 114 | 104 | 91.2281 | |
| jmaeng-gatk | SNP | ti | HG002compoundhet | het | 99.3342 | 98.8953 | 99.7771 | 40.7782 | 9400 | 105 | 9400 | 21 | 17 | 80.9524 | |
| ltrigg-rtg2 | SNP | ti | HG002compoundhet | het | 99.3400 | 99.0005 | 99.6817 | 37.0509 | 9410 | 95 | 9396 | 30 | 8 | 26.6667 | |
| qzeng-custom | INDEL | I1_5 | HG002compoundhet | * | 82.4804 | 75.6151 | 90.7168 | 64.6037 | 9343 | 3013 | 9391 | 961 | 822 | 85.5359 | |
| hfeng-pmm2 | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.3601 | 96.8531 | 99.9148 | 65.6503 | 9387 | 305 | 9387 | 8 | 5 | 62.5000 | |
| asubramanian-gatk | SNP | * | map_l125_m1_e0 | het | 49.6482 | 33.0516 | 99.7236 | 92.3828 | 9384 | 19008 | 9381 | 26 | 6 | 23.0769 | |
| mlin-fermikit | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.0726 | 96.5229 | 95.6265 | 68.5165 | 9355 | 337 | 9380 | 429 | 282 | 65.7343 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.9905 | 98.3405 | 99.6492 | 44.7855 | 9363 | 158 | 9375 | 33 | 31 | 93.9394 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 66.4593 | 77.1439 | 58.3743 | 42.1879 | 6477 | 1919 | 9372 | 6683 | 5135 | 76.8367 | |
| anovak-vg | SNP | tv | map_l150_m1_e0 | * | 79.0094 | 85.9421 | 73.1117 | 78.8881 | 9378 | 1534 | 9370 | 3446 | 807 | 23.4185 | |
| ckim-vqsr | SNP | ti | HG002compoundhet | het | 99.2006 | 98.5692 | 99.8402 | 40.6564 | 9369 | 136 | 9369 | 15 | 13 | 86.6667 | |
| dgrover-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.9925 | 94.4604 | 95.5306 | 69.2327 | 9515 | 558 | 9362 | 438 | 390 | 89.0411 | |
| astatham-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.9849 | 94.4009 | 95.5762 | 69.0899 | 9509 | 564 | 9355 | 433 | 393 | 90.7621 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 83.9007 | 77.8470 | 90.9754 | 41.3740 | 8627 | 2455 | 9355 | 928 | 916 | 98.7069 | |
| astatham-gatk | SNP | ti | map_l150_m1_e0 | het | 85.9873 | 75.6508 | 99.5954 | 82.9552 | 9358 | 3012 | 9354 | 38 | 18 | 47.3684 | |
| jlack-gatk | INDEL | D1_5 | * | hetalt | 95.0041 | 90.9322 | 99.4577 | 62.5612 | 9316 | 929 | 9354 | 51 | 46 | 90.1961 | |
| ciseli-custom | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 78.8703 | 94.8102 | 67.5188 | 69.4075 | 9189 | 503 | 9350 | 4498 | 362 | 8.0480 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 88.6540 | 89.8499 | 87.4895 | 45.7726 | 8498 | 960 | 9343 | 1336 | 702 | 52.5449 | |
| gduggal-bwavard | INDEL | D1_5 | HG002complexvar | homalt | 96.6460 | 93.8290 | 99.6373 | 42.9597 | 9944 | 654 | 9340 | 34 | 22 | 64.7059 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 92.4596 | 98.1094 | 87.4251 | 55.1844 | 9341 | 180 | 9337 | 1343 | 1337 | 99.5532 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 80.3927 | 81.2870 | 79.5178 | 59.9939 | 9335 | 2149 | 9333 | 2404 | 2119 | 88.1448 | |
| anovak-vg | SNP | ti | map_l125_m2_e1 | homalt | 90.0123 | 82.2569 | 99.3822 | 67.2869 | 9425 | 2033 | 9330 | 58 | 53 | 91.3793 | |
| ckim-gatk | SNP | ti | map_l150_m1_e0 | het | 84.9286 | 75.4406 | 97.1464 | 89.3093 | 9332 | 3038 | 9328 | 274 | 32 | 11.6788 | |
| gduggal-snapvard | INDEL | D1_5 | HG002complexvar | homalt | 91.8287 | 87.2523 | 96.9117 | 42.9901 | 9247 | 1351 | 9320 | 297 | 279 | 93.9394 | |
| mlin-fermikit | INDEL | I6_15 | * | het | 88.6098 | 92.6243 | 84.9289 | 50.1273 | 9293 | 740 | 9315 | 1653 | 1640 | 99.2136 | |
| ckim-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.7342 | 93.9641 | 95.5170 | 68.9673 | 9465 | 608 | 9311 | 437 | 395 | 90.3890 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.3347 | 93.7357 | 96.9893 | 65.2412 | 9442 | 631 | 9310 | 289 | 255 | 88.2353 | |
| jmaeng-gatk | SNP | ti | map_l150_m1_e0 | het | 84.7465 | 75.2789 | 96.9381 | 89.5763 | 9312 | 3058 | 9308 | 294 | 33 | 11.2245 | |
| egarrison-hhga | SNP | ti | HG002compoundhet | het | 98.7211 | 97.8643 | 99.5931 | 37.6968 | 9302 | 203 | 9300 | 38 | 21 | 55.2632 | |