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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
60601-60650 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | D1_5 | HG002compoundhet | * | 95.6235 | 92.5950 | 98.8568 | 63.0617 | 11329 | 906 | 11328 | 131 | 126 | 96.1832 | |
| gduggal-bwafb | SNP | * | func_cds | het | 99.3985 | 99.9462 | 98.8568 | 33.7832 | 11155 | 6 | 11155 | 129 | 2 | 1.5504 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 60.3108 | 43.3915 | 98.8571 | 88.9937 | 174 | 227 | 173 | 2 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 97.6832 | 96.5368 | 98.8571 | 39.8625 | 446 | 16 | 173 | 2 | 2 | 100.0000 | |
| jlack-gatk | INDEL | * | map_l100_m1_e0 | homalt | 98.7765 | 98.6960 | 98.8571 | 82.9030 | 1211 | 16 | 1211 | 14 | 6 | 42.8571 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l125_m1_e0 | homalt | 98.9986 | 99.1404 | 98.8571 | 84.4858 | 346 | 3 | 346 | 4 | 4 | 100.0000 | |
| hfeng-pmm1 | SNP | * | map_l250_m2_e0 | het | 98.5614 | 98.2672 | 98.8573 | 88.7531 | 5104 | 90 | 5104 | 59 | 11 | 18.6441 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 99.0461 | 99.2354 | 98.8575 | 51.9477 | 1817 | 14 | 1817 | 21 | 0 | 0.0000 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.4677 | 98.0807 | 98.8578 | 41.0102 | 24069 | 471 | 24060 | 278 | 268 | 96.4029 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.1286 | 95.4588 | 98.8579 | 46.1719 | 13159 | 626 | 13157 | 152 | 147 | 96.7105 | |
| ghariani-varprowl | SNP | ti | * | het | 99.3626 | 99.8721 | 98.8582 | 25.2183 | 1280237 | 1639 | 1280417 | 14789 | 277 | 1.8730 | |
| ckim-isaac | INDEL | D16_PLUS | HG002compoundhet | hetalt | 86.1574 | 76.3485 | 98.8582 | 24.5694 | 1472 | 456 | 1645 | 19 | 17 | 89.4737 | |
| hfeng-pmm2 | SNP | ti | map_l250_m0_e0 | homalt | 99.0847 | 99.3119 | 98.8584 | 92.1786 | 433 | 3 | 433 | 5 | 2 | 40.0000 | |
| hfeng-pmm1 | SNP | ti | map_l250_m0_e0 | homalt | 99.0847 | 99.3119 | 98.8584 | 92.1786 | 433 | 3 | 433 | 5 | 2 | 40.0000 | |
| hfeng-pmm3 | SNP | ti | map_l250_m0_e0 | homalt | 99.0847 | 99.3119 | 98.8584 | 92.1463 | 433 | 3 | 433 | 5 | 2 | 40.0000 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.8162 | 92.9554 | 98.8588 | 48.8601 | 2771 | 210 | 2772 | 32 | 27 | 84.3750 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.3820 | 97.9096 | 98.8590 | 53.4408 | 5480 | 117 | 13083 | 151 | 132 | 87.4172 | |
| ltrigg-rtg1 | INDEL | * | map_l100_m0_e0 | * | 96.4953 | 94.2418 | 98.8591 | 79.2883 | 1473 | 90 | 1473 | 17 | 4 | 23.5294 | |
| ltrigg-rtg2 | INDEL | I1_5 | map_l100_m0_e0 | * | 97.5715 | 96.3168 | 98.8593 | 76.8994 | 523 | 20 | 520 | 6 | 1 | 16.6667 | |
| rpoplin-dv42 | INDEL | I1_5 | map_l150_m2_e1 | * | 98.2012 | 97.5518 | 98.8593 | 89.9733 | 518 | 13 | 520 | 6 | 2 | 33.3333 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.2667 | 91.9260 | 98.8593 | 33.2487 | 2334 | 205 | 2860 | 33 | 31 | 93.9394 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5115 | 98.1663 | 98.8593 | 41.0712 | 24090 | 450 | 24092 | 278 | 270 | 97.1223 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.5454 | 98.2333 | 98.8594 | 76.8466 | 2947 | 53 | 2947 | 34 | 5 | 14.7059 | |
| ckim-isaac | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.5147 | 94.2784 | 98.8597 | 54.0704 | 52448 | 3183 | 52797 | 609 | 355 | 58.2923 | |
| gduggal-snapplat | SNP | * | segdup | het | 98.6817 | 98.5044 | 98.8598 | 94.8279 | 17058 | 259 | 17080 | 197 | 17 | 8.6294 | |
| gduggal-bwafb | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 98.9805 | 99.1013 | 98.8599 | 68.0375 | 1213 | 11 | 1214 | 14 | 8 | 57.1429 | |
| gduggal-bwavard | SNP | tv | segdup | * | 98.0164 | 97.1871 | 98.8601 | 94.3820 | 8292 | 240 | 8239 | 95 | 34 | 35.7895 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 77.7475 | 64.0656 | 98.8601 | 79.0638 | 2266 | 1271 | 2255 | 26 | 19 | 73.0769 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 68.6110 | 52.5360 | 98.8604 | 77.0138 | 694 | 627 | 694 | 8 | 6 | 75.0000 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 92.8267 | 87.4867 | 98.8609 | 64.0750 | 1650 | 236 | 1649 | 19 | 5 | 26.3158 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.0580 | 99.2555 | 98.8612 | 71.4717 | 3733 | 28 | 3733 | 43 | 43 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.0580 | 99.2555 | 98.8612 | 71.4717 | 3733 | 28 | 3733 | 43 | 43 | 100.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.6707 | 96.5079 | 98.8618 | 65.9091 | 608 | 22 | 608 | 7 | 5 | 71.4286 | |
| astatham-gatk | INDEL | I1_5 | map_l125_m1_e0 | * | 96.3571 | 93.9759 | 98.8622 | 86.8583 | 780 | 50 | 782 | 9 | 2 | 22.2222 | |
| gduggal-snapfb | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.2467 | 99.6334 | 98.8630 | 62.3274 | 10871 | 40 | 10869 | 125 | 24 | 19.2000 | |
| ckim-vqsr | SNP | ti | map_l150_m2_e0 | * | 66.8194 | 50.4631 | 98.8632 | 91.2397 | 10351 | 10161 | 10349 | 119 | 3 | 2.5210 | |
| ckim-isaac | INDEL | I1_5 | map_l125_m2_e0 | * | 82.6884 | 71.0618 | 98.8636 | 87.6156 | 609 | 248 | 609 | 7 | 2 | 28.5714 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.4286 | 100.0000 | 98.8636 | 81.1159 | 87 | 0 | 87 | 1 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | I6_15 | map_l100_m2_e0 | * | 86.3981 | 76.7241 | 98.8636 | 82.8460 | 89 | 27 | 87 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | I6_15 | map_l100_m2_e1 | * | 86.3981 | 76.7241 | 98.8636 | 83.1740 | 89 | 27 | 87 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | INDEL | * | map_l125_m1_e0 | het | 78.5553 | 65.1685 | 98.8636 | 94.8423 | 870 | 465 | 870 | 10 | 2 | 20.0000 | |
| gduggal-snapfb | INDEL | D1_5 | map_l100_m2_e1 | homalt | 98.4625 | 98.0645 | 98.8636 | 87.2332 | 608 | 12 | 609 | 7 | 5 | 71.4286 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 72.1992 | 56.8627 | 98.8636 | 64.0816 | 87 | 66 | 87 | 1 | 1 | 100.0000 | |
| jpowers-varprowl | INDEL | D1_5 | map_l125_m2_e1 | homalt | 96.1326 | 93.5484 | 98.8636 | 82.1138 | 348 | 24 | 348 | 4 | 1 | 25.0000 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 86.8187 | 77.3900 | 98.8636 | 65.8694 | 510 | 149 | 522 | 6 | 6 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 86.8187 | 77.3900 | 98.8636 | 65.8694 | 510 | 149 | 522 | 6 | 6 | 100.0000 | |
| ckim-isaac | INDEL | * | map_l150_m2_e1 | homalt | 69.0476 | 53.0488 | 98.8636 | 85.5104 | 261 | 231 | 261 | 3 | 1 | 33.3333 | |
| cchapple-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.6739 | 98.4848 | 98.8636 | 88.6158 | 65 | 1 | 87 | 1 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 64.6644 | 48.0447 | 98.8636 | 26.6667 | 86 | 93 | 87 | 1 | 1 | 100.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.4286 | 100.0000 | 98.8636 | 79.0974 | 87 | 0 | 87 | 1 | 0 | 0.0000 | |