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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
4901-4950 / 86044 show all | |||||||||||||||
| qzeng-custom | INDEL | I1_5 | * | homalt | 99.1725 | 99.1196 | 99.2255 | 48.3268 | 59896 | 532 | 59833 | 467 | 326 | 69.8073 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 64.6148 | 54.0919 | 80.2207 | 60.1084 | 1236 | 1049 | 1890 | 466 | 171 | 36.6953 | |
| hfeng-pmm2 | SNP | tv | * | het | 99.8886 | 99.8560 | 99.9212 | 22.0414 | 590844 | 852 | 590770 | 466 | 18 | 3.8627 | |
| rpoplin-dv42 | INDEL | D6_15 | * | het | 97.5270 | 99.0079 | 96.0896 | 61.5469 | 11477 | 115 | 11451 | 466 | 447 | 95.9227 | |
| ckim-vqsr | INDEL | * | HG002compoundhet | het | 93.3882 | 98.2169 | 89.0120 | 79.6916 | 4021 | 73 | 3775 | 466 | 457 | 98.0687 | |
| anovak-vg | INDEL | I1_5 | map_l100_m2_e1 | homalt | 67.1322 | 92.7778 | 52.5941 | 79.0940 | 501 | 39 | 517 | 466 | 438 | 93.9914 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5463 | 98.3740 | 98.7193 | 52.5147 | 35997 | 595 | 35921 | 466 | 435 | 93.3476 | |
| asubramanian-gatk | INDEL | D6_15 | * | * | 97.6552 | 97.1179 | 98.1984 | 55.4499 | 25340 | 752 | 25346 | 465 | 420 | 90.3226 | |
| hfeng-pmm2 | SNP | * | map_siren | * | 99.6789 | 99.6758 | 99.6819 | 56.1450 | 145754 | 474 | 145731 | 465 | 62 | 13.3333 | |
| qzeng-custom | SNP | ti | map_l125_m1_e0 | het | 82.7364 | 72.3585 | 96.5897 | 86.1572 | 13217 | 5049 | 13170 | 465 | 385 | 82.7957 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 82.2315 | 84.9860 | 79.6499 | 75.4433 | 1817 | 321 | 1820 | 465 | 124 | 26.6667 | |
| gduggal-snapvard | INDEL | * | map_l150_m2_e0 | het | 82.4377 | 96.1369 | 72.1557 | 91.9661 | 871 | 35 | 1205 | 465 | 145 | 31.1828 | |
| gduggal-snapfb | SNP | tv | map_l150_m2_e1 | * | 96.3446 | 96.7049 | 95.9869 | 79.3609 | 11123 | 379 | 11122 | 465 | 180 | 38.7097 | |
| ghariani-varprowl | INDEL | * | map_l100_m2_e1 | * | 90.3178 | 92.5453 | 88.1950 | 92.4782 | 3476 | 280 | 3474 | 465 | 216 | 46.4516 | |
| ghariani-varprowl | SNP | tv | map_l150_m1_e0 | het | 96.2185 | 98.9058 | 93.6733 | 82.5202 | 6870 | 76 | 6870 | 464 | 74 | 15.9483 | |
| ciseli-custom | INDEL | * | map_l125_m1_e0 | * | 67.4524 | 62.0788 | 73.8444 | 90.3002 | 1308 | 799 | 1310 | 464 | 300 | 64.6552 | |
| ciseli-custom | SNP | tv | map_l250_m1_e0 | het | 59.5668 | 53.4415 | 67.2779 | 93.2143 | 955 | 832 | 954 | 464 | 21 | 4.5259 | |
| jlack-gatk | SNP | ti | map_l250_m1_e0 | het | 91.8885 | 98.2817 | 86.2762 | 93.7627 | 2917 | 51 | 2917 | 464 | 39 | 8.4052 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 73.2802 | 81.7861 | 66.3768 | 81.5483 | 696 | 155 | 916 | 464 | 182 | 39.2241 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.3493 | 98.1589 | 98.5404 | 55.2323 | 31403 | 589 | 31326 | 464 | 446 | 96.1207 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 79.2712 | 87.6596 | 72.3480 | 57.0624 | 1236 | 174 | 1214 | 464 | 433 | 93.3190 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 97.1997 | 99.7848 | 94.7452 | 59.6307 | 8348 | 18 | 8348 | 463 | 461 | 99.5680 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 75.3026 | 95.6815 | 62.0803 | 56.2366 | 709 | 32 | 758 | 463 | 445 | 96.1123 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.1130 | 95.4143 | 96.8220 | 50.6721 | 14107 | 678 | 14106 | 463 | 453 | 97.8402 | |
| gduggal-bwafb | SNP | ti | HG002compoundhet | het | 96.9467 | 98.6218 | 95.3275 | 45.8199 | 9374 | 131 | 9446 | 463 | 78 | 16.8467 | |
| gduggal-bwavard | INDEL | * | map_l100_m2_e0 | * | 90.5115 | 93.0138 | 88.1404 | 88.0002 | 3435 | 258 | 3441 | 463 | 191 | 41.2527 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 79.1180 | 67.8700 | 94.8349 | 76.6136 | 8498 | 4023 | 8501 | 463 | 140 | 30.2376 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 85.0370 | 96.2351 | 76.1733 | 88.6760 | 1457 | 57 | 1477 | 462 | 66 | 14.2857 | |
| anovak-vg | INDEL | I1_5 | segdup | * | 58.1085 | 58.4514 | 57.7697 | 94.2442 | 619 | 440 | 632 | 462 | 397 | 85.9307 | |
| anovak-vg | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 96.2926 | 96.8040 | 95.7866 | 41.7994 | 10389 | 343 | 10503 | 462 | 244 | 52.8139 | |
| jpowers-varprowl | SNP | * | HG002compoundhet | het | 94.4520 | 92.3614 | 96.6395 | 53.1760 | 13095 | 1083 | 13286 | 462 | 40 | 8.6580 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 71.5827 | 62.3493 | 84.0263 | 65.9228 | 2431 | 1468 | 2425 | 461 | 430 | 93.2755 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 80.3562 | 86.2869 | 75.1884 | 83.1152 | 1227 | 195 | 1397 | 461 | 231 | 50.1085 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.7947 | 99.0383 | 98.5524 | 55.6705 | 16271 | 158 | 31384 | 461 | 49 | 10.6291 | |
| gduggal-snapfb | SNP | tv | map_l150_m2_e0 | * | 96.3189 | 96.6711 | 95.9692 | 79.3481 | 10977 | 378 | 10976 | 461 | 180 | 39.0456 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.3306 | 96.7640 | 97.9038 | 49.8941 | 21530 | 720 | 21531 | 461 | 429 | 93.0586 | |
| ckim-isaac | INDEL | D6_15 | HG002complexvar | * | 83.7635 | 78.4798 | 89.8099 | 48.6609 | 4161 | 1141 | 4063 | 461 | 184 | 39.9132 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 64.3273 | 59.5954 | 69.8756 | 29.2072 | 1031 | 699 | 1067 | 460 | 370 | 80.4348 | |
| jpowers-varprowl | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 94.1706 | 97.3744 | 91.1708 | 74.9459 | 4710 | 127 | 4750 | 460 | 136 | 29.5652 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 95.3424 | 98.3065 | 92.5518 | 69.4000 | 5747 | 99 | 5716 | 460 | 444 | 96.5217 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 95.3424 | 98.3065 | 92.5518 | 69.4000 | 5747 | 99 | 5716 | 460 | 444 | 96.5217 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 58.9132 | 46.9890 | 78.9474 | 83.7848 | 1662 | 1875 | 1725 | 460 | 86 | 18.6957 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 38.8523 | 42.9872 | 35.4430 | 84.3564 | 236 | 313 | 252 | 459 | 4 | 0.8715 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 93.1339 | 90.7869 | 95.6056 | 36.5855 | 10061 | 1021 | 9986 | 459 | 410 | 89.3246 | |
| gduggal-bwavard | INDEL | * | map_l100_m1_e0 | * | 90.3615 | 92.9448 | 87.9179 | 87.2169 | 3333 | 253 | 3340 | 459 | 189 | 41.1765 | |
| hfeng-pmm3 | INDEL | * | HG002compoundhet | homalt | 74.6579 | 99.4169 | 59.7721 | 77.4506 | 682 | 4 | 682 | 459 | 454 | 98.9107 | |
| ciseli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 84.1283 | 97.5299 | 73.9648 | 66.0177 | 1303 | 33 | 1304 | 459 | 12 | 2.6144 | |
| ciseli-custom | INDEL | D16_PLUS | HG002complexvar | homalt | 50.2549 | 88.5813 | 35.0778 | 60.5689 | 256 | 33 | 248 | 459 | 398 | 86.7102 | |
| eyeh-varpipe | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | het | 96.5155 | 99.7628 | 93.4730 | 54.4025 | 6728 | 16 | 6559 | 458 | 33 | 7.2052 | |
| eyeh-varpipe | SNP | tv | map_l125_m0_e0 | * | 96.4575 | 99.6230 | 93.4869 | 79.0795 | 6606 | 25 | 6574 | 458 | 11 | 2.4018 | |