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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
72901-72950 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.9340 | 99.3274 | 98.5437 | 62.8374 | 15654 | 106 | 15496 | 229 | 203 | 88.6463 | |
| gduggal-bwafb | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 81.8128 | 74.8933 | 90.1411 | 58.1664 | 7544 | 2529 | 8942 | 978 | 867 | 88.6503 | |
| mlin-fermikit | SNP | ti | segdup | homalt | 98.7142 | 98.7209 | 98.7075 | 85.2139 | 7409 | 96 | 7408 | 97 | 86 | 88.6598 | |
| mlin-fermikit | SNP | ti | map_l150_m1_e0 | * | 56.8574 | 42.3346 | 86.5470 | 60.8408 | 8345 | 11367 | 8344 | 1297 | 1150 | 88.6662 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 56.5337 | 42.2760 | 85.3023 | 63.5610 | 1538 | 2100 | 1538 | 265 | 235 | 88.6792 | |
| ghariani-varprowl | INDEL | D6_15 | map_siren | het | 83.2073 | 98.2143 | 72.1785 | 87.9583 | 275 | 5 | 275 | 106 | 94 | 88.6792 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.1557 | 94.5865 | 89.8467 | 85.0129 | 629 | 36 | 469 | 53 | 47 | 88.6792 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.8775 | 93.1174 | 92.6389 | 73.8277 | 690 | 51 | 667 | 53 | 47 | 88.6792 | |
| jpowers-varprowl | INDEL | I1_5 | * | homalt | 94.7762 | 91.6661 | 98.1046 | 39.3198 | 55392 | 5036 | 55332 | 1069 | 948 | 88.6810 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 96.0150 | 95.3702 | 96.6686 | 70.3632 | 4882 | 237 | 4875 | 168 | 149 | 88.6905 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 62.3368 | 46.0175 | 96.5915 | 42.2906 | 1687 | 1979 | 1757 | 62 | 55 | 88.7097 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 75.5916 | 74.7677 | 76.4339 | 43.0667 | 1609 | 543 | 1839 | 567 | 503 | 88.7125 | |
| anovak-vg | INDEL | I6_15 | * | homalt | 61.4755 | 80.7661 | 49.6232 | 33.6435 | 5039 | 1200 | 5202 | 5281 | 4685 | 88.7143 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 89.5657 | 94.4378 | 85.1716 | 64.2887 | 7895 | 465 | 7892 | 1374 | 1219 | 88.7191 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 89.5657 | 94.4378 | 85.1716 | 64.2887 | 7895 | 465 | 7892 | 1374 | 1219 | 88.7191 | |
| ckim-isaac | INDEL | I16_PLUS | HG002compoundhet | het | 19.1083 | 31.9149 | 13.6364 | 72.1014 | 15 | 32 | 21 | 133 | 118 | 88.7218 | |
| jlack-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.4559 | 95.1485 | 89.9115 | 78.4139 | 3844 | 196 | 3556 | 399 | 354 | 88.7218 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 28.5107 | 24.0260 | 35.0540 | 65.4357 | 296 | 936 | 292 | 541 | 480 | 88.7246 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.0894 | 96.6856 | 99.5346 | 57.0832 | 30367 | 1041 | 30368 | 142 | 126 | 88.7324 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.0894 | 96.6856 | 99.5346 | 57.0832 | 30367 | 1041 | 30368 | 142 | 126 | 88.7324 | |
| egarrison-hhga | INDEL | I6_15 | * | hetalt | 95.1738 | 91.5448 | 99.1023 | 37.9004 | 7828 | 723 | 7838 | 71 | 63 | 88.7324 | |
| mlin-fermikit | INDEL | D1_5 | map_l150_m2_e0 | * | 66.8704 | 54.9148 | 85.4806 | 82.9140 | 419 | 344 | 418 | 71 | 63 | 88.7324 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 85.7255 | 84.9037 | 86.5634 | 80.2326 | 36793 | 6542 | 37456 | 5814 | 5159 | 88.7341 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 94.9783 | 96.9173 | 93.1153 | 84.1668 | 1289 | 41 | 1082 | 80 | 71 | 88.7500 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.1165 | 95.7477 | 98.5251 | 68.8562 | 5359 | 238 | 5344 | 80 | 71 | 88.7500 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 76.6125 | 83.7838 | 70.5720 | 29.6655 | 589 | 114 | 1024 | 427 | 379 | 88.7588 | |
| mlin-fermikit | SNP | ti | map_l125_m1_e0 | * | 63.1485 | 49.0745 | 88.5410 | 56.6927 | 14396 | 14939 | 14395 | 1863 | 1654 | 88.7815 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.5010 | 99.4006 | 99.6016 | 52.3483 | 25207 | 152 | 26749 | 107 | 95 | 88.7850 | |
| mlin-fermikit | INDEL | D16_PLUS | * | homalt | 91.6240 | 96.0993 | 87.5470 | 75.8209 | 1626 | 66 | 1631 | 232 | 206 | 88.7931 | |
| jpowers-varprowl | INDEL | I6_15 | HG002complexvar | homalt | 84.7204 | 80.4778 | 89.4353 | 51.1131 | 977 | 237 | 982 | 116 | 103 | 88.7931 | |
| egarrison-hhga | INDEL | I6_15 | HG002compoundhet | homalt | 19.2440 | 90.3226 | 10.7692 | 63.7883 | 28 | 3 | 28 | 232 | 206 | 88.7931 | |
| mlin-fermikit | INDEL | I1_5 | map_siren | * | 83.5106 | 74.6755 | 94.7168 | 75.2199 | 2244 | 761 | 2241 | 125 | 111 | 88.8000 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.6238 | 99.4640 | 97.7977 | 72.6194 | 5567 | 30 | 5551 | 125 | 111 | 88.8000 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 91.6583 | 85.8616 | 98.2945 | 30.7003 | 8994 | 1481 | 9279 | 161 | 143 | 88.8199 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 58.2286 | 59.3301 | 57.1672 | 32.0973 | 248 | 170 | 335 | 251 | 223 | 88.8446 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 66.7314 | 81.9672 | 56.2718 | 32.0710 | 100 | 22 | 323 | 251 | 223 | 88.8446 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 47.7941 | 75.5844 | 34.9456 | 64.9725 | 291 | 94 | 289 | 538 | 478 | 88.8476 | |
| bgallagher-sentieon | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.0261 | 98.9285 | 99.1239 | 73.3821 | 93437 | 1012 | 93346 | 825 | 733 | 88.8485 | |
| raldana-dualsentieon | INDEL | * | * | * | 99.1095 | 98.7566 | 99.4648 | 57.7282 | 340258 | 4284 | 340120 | 1830 | 1626 | 88.8525 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.2830 | 96.3585 | 98.2253 | 48.3467 | 19846 | 750 | 19870 | 359 | 319 | 88.8579 | |
| ciseli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 76.6853 | 89.2624 | 67.2148 | 71.4466 | 27458 | 3303 | 27386 | 13358 | 11870 | 88.8606 | |
| mlin-fermikit | INDEL | D1_5 | HG002complexvar | het | 96.8827 | 95.7525 | 98.0399 | 50.2469 | 19883 | 882 | 19757 | 395 | 351 | 88.8608 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.8701 | 97.6006 | 98.1411 | 68.2416 | 63783 | 1568 | 63513 | 1203 | 1069 | 88.8612 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.8701 | 97.6006 | 98.1411 | 68.2416 | 63783 | 1568 | 63513 | 1203 | 1069 | 88.8612 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.1835 | 98.9169 | 97.4610 | 70.8771 | 17626 | 193 | 17235 | 449 | 399 | 88.8641 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.1522 | 95.1464 | 99.2443 | 33.7229 | 1137 | 58 | 1182 | 9 | 8 | 88.8889 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0727 | 99.1931 | 98.9527 | 67.4865 | 13646 | 111 | 13605 | 144 | 128 | 88.8889 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0727 | 99.1931 | 98.9527 | 67.4865 | 13646 | 111 | 13605 | 144 | 128 | 88.8889 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.7600 | 86.9438 | 99.4102 | 29.9035 | 1485 | 223 | 1517 | 9 | 8 | 88.8889 | |
| astatham-gatk | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.9155 | 97.9955 | 99.8529 | 70.5060 | 6111 | 125 | 6111 | 9 | 8 | 88.8889 | |