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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
62701-62750 / 86044 show all | |||||||||||||||
| asubramanian-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.5619 | 97.6596 | 99.4810 | 64.5181 | 459 | 11 | 575 | 3 | 3 | 100.0000 | |
| rpoplin-dv42 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 90.6947 | 87.3874 | 94.2623 | 81.0323 | 582 | 84 | 575 | 35 | 32 | 91.4286 | |
| rpoplin-dv42 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 90.6947 | 87.3874 | 94.2623 | 81.0323 | 582 | 84 | 575 | 35 | 32 | 91.4286 | |
| jlack-gatk | SNP | ti | HG002compoundhet | hetalt | 99.6534 | 99.3092 | 100.0000 | 21.8750 | 575 | 4 | 575 | 0 | 0 | ||
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 91.9041 | 90.7937 | 93.0421 | 69.1771 | 572 | 58 | 575 | 43 | 30 | 69.7674 | |
| gduggal-bwavard | INDEL | * | map_l125_m0_e0 | het | 86.9907 | 98.1261 | 78.1250 | 92.7637 | 576 | 11 | 575 | 161 | 28 | 17.3913 | |
| gduggal-bwafb | INDEL | D1_5 | map_l100_m0_e0 | het | 97.1284 | 97.1235 | 97.1332 | 84.0205 | 574 | 17 | 576 | 17 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | D1_5 | map_l100_m2_e0 | homalt | 96.7204 | 94.1080 | 99.4819 | 84.5641 | 575 | 36 | 576 | 3 | 1 | 33.3333 | |
| bgallagher-sentieon | SNP | ti | HG002compoundhet | hetalt | 99.7403 | 99.4819 | 100.0000 | 21.8453 | 576 | 3 | 576 | 0 | 0 | ||
| jpowers-varprowl | INDEL | D1_5 | map_l100_m2_e1 | homalt | 95.8403 | 92.9032 | 98.9691 | 78.1695 | 576 | 44 | 576 | 6 | 2 | 33.3333 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.9721 | 86.8671 | 100.0000 | 38.2637 | 549 | 83 | 576 | 0 | 0 | ||
| eyeh-varpipe | INDEL | * | HG002compoundhet | homalt | 7.7309 | 93.0029 | 4.0330 | 55.0612 | 638 | 48 | 576 | 13706 | 13667 | 99.7155 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m2_e1 | homalt | 95.2066 | 92.9032 | 97.6271 | 78.5766 | 576 | 44 | 576 | 14 | 2 | 14.2857 | |
| hfeng-pmm3 | INDEL | * | map_l125_m0_e0 | het | 97.7062 | 97.7853 | 97.6271 | 88.4968 | 574 | 13 | 576 | 14 | 2 | 14.2857 | |
| hfeng-pmm2 | INDEL | * | map_l125_m0_e0 | het | 96.7218 | 97.7853 | 95.6811 | 90.4293 | 574 | 13 | 576 | 26 | 2 | 7.6923 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.2235 | 98.4589 | 100.0000 | 19.2146 | 575 | 9 | 576 | 0 | 0 | ||
| rpoplin-dv42 | INDEL | D1_5 | map_l100_m0_e0 | het | 97.7076 | 97.2927 | 98.1261 | 84.3425 | 575 | 16 | 576 | 11 | 2 | 18.1818 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.9133 | 100.0000 | 99.8267 | 69.4709 | 576 | 0 | 576 | 1 | 0 | 0.0000 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.8216 | 96.0549 | 99.6546 | 66.2784 | 560 | 23 | 577 | 2 | 2 | 100.0000 | |
| egarrison-hhga | SNP | ti | * | hetalt | 98.9708 | 99.1409 | 98.8014 | 49.0846 | 577 | 5 | 577 | 7 | 7 | 100.0000 | |
| dgrover-gatk | SNP | ti | HG002compoundhet | hetalt | 99.8270 | 99.6546 | 100.0000 | 22.2372 | 577 | 2 | 577 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | * | map_l125_m0_e0 | het | 97.0529 | 97.9557 | 96.1667 | 90.6074 | 575 | 12 | 577 | 23 | 2 | 8.6957 | |
| astatham-gatk | SNP | ti | HG002compoundhet | hetalt | 99.8270 | 99.6546 | 100.0000 | 21.9215 | 577 | 2 | 577 | 0 | 0 | ||
| mlin-fermikit | INDEL | I16_PLUS | HG002complexvar | het | 86.1405 | 88.2707 | 84.1108 | 65.5276 | 587 | 78 | 577 | 109 | 105 | 96.3303 | |
| ltrigg-rtg2 | SNP | ti | HG002compoundhet | hetalt | 99.7403 | 99.4819 | 100.0000 | 21.4966 | 576 | 3 | 577 | 0 | 0 | ||
| qzeng-custom | INDEL | I1_5 | map_l100_m0_e0 | * | 78.8389 | 67.0350 | 95.6882 | 90.8414 | 364 | 179 | 577 | 26 | 10 | 38.4615 | |
| gduggal-bwaplat | INDEL | I1_5 | map_l100_m2_e0 | het | 83.8663 | 72.7617 | 98.9708 | 93.0529 | 577 | 216 | 577 | 6 | 1 | 16.6667 | |
| gduggal-bwaplat | SNP | ti | map_l250_m2_e1 | homalt | 49.1915 | 32.6185 | 100.0000 | 95.2072 | 578 | 1194 | 577 | 0 | 0 | ||
| gduggal-bwavard | INDEL | D1_5 | map_l100_m0_e0 | het | 89.9509 | 98.4772 | 82.7834 | 89.5125 | 582 | 9 | 577 | 120 | 17 | 14.1667 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m2_e1 | homalt | 97.1870 | 94.8387 | 99.6546 | 75.9352 | 588 | 32 | 577 | 2 | 2 | 100.0000 | |
| jli-custom | SNP | ti | HG002compoundhet | hetalt | 99.8270 | 99.6546 | 100.0000 | 22.4462 | 577 | 2 | 577 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 97.5413 | 96.6355 | 98.4642 | 83.8745 | 517 | 18 | 577 | 9 | 9 | 100.0000 | |
| raldana-dualsentieon | SNP | ti | HG002compoundhet | hetalt | 99.8270 | 99.6546 | 100.0000 | 21.4966 | 577 | 2 | 577 | 0 | 0 | ||
| hfeng-pmm2 | SNP | ti | HG002compoundhet | hetalt | 99.8270 | 99.6546 | 100.0000 | 22.7577 | 577 | 2 | 577 | 0 | 0 | ||
| hfeng-pmm1 | SNP | ti | HG002compoundhet | hetalt | 99.8270 | 99.6546 | 100.0000 | 22.5503 | 577 | 2 | 577 | 0 | 0 | ||
| hfeng-pmm3 | SNP | ti | HG002compoundhet | hetalt | 99.8270 | 99.6546 | 100.0000 | 22.4462 | 577 | 2 | 577 | 0 | 0 | ||
| jlack-gatk | SNP | ti | * | hetalt | 98.8034 | 99.3127 | 98.2993 | 52.8846 | 578 | 4 | 578 | 10 | 10 | 100.0000 | |
| gduggal-bwafb | SNP | ti | HG002compoundhet | hetalt | 99.9136 | 99.8273 | 100.0000 | 23.3422 | 578 | 1 | 578 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 69.9400 | 54.1784 | 98.6348 | 79.3006 | 577 | 488 | 578 | 8 | 7 | 87.5000 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 95.7178 | 94.6429 | 96.8174 | 68.4294 | 583 | 33 | 578 | 19 | 17 | 89.4737 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 91.3367 | 84.1772 | 99.8273 | 38.7302 | 532 | 100 | 578 | 1 | 1 | 100.0000 | |
| ckim-dragen | SNP | ti | HG002compoundhet | hetalt | 99.9136 | 99.8273 | 100.0000 | 21.5739 | 578 | 1 | 578 | 0 | 0 | ||
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.3971 | 98.8014 | 100.0000 | 18.5915 | 577 | 7 | 578 | 0 | 0 | ||
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.3971 | 98.8014 | 100.0000 | 18.5915 | 577 | 7 | 578 | 0 | 0 | ||
| egarrison-hhga | INDEL | D1_5 | map_l100_m0_e0 | het | 97.4705 | 97.8003 | 97.1429 | 84.6491 | 578 | 13 | 578 | 17 | 3 | 17.6471 | |
| ndellapenna-hhga | INDEL | D16_PLUS | HG002compoundhet | het | 77.8675 | 83.4568 | 72.9798 | 46.7026 | 338 | 67 | 578 | 214 | 199 | 92.9907 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.3981 | 98.9726 | 99.8273 | 17.0487 | 578 | 6 | 578 | 1 | 1 | 100.0000 | |
| rpoplin-dv42 | SNP | ti | HG002compoundhet | hetalt | 99.9136 | 99.8273 | 100.0000 | 21.6802 | 578 | 1 | 578 | 0 | 0 | ||
| ghariani-varprowl | INDEL | I16_PLUS | HG002complexvar | het | 78.0918 | 86.6165 | 71.0947 | 66.0117 | 576 | 89 | 578 | 235 | 228 | 97.0213 | |
| gduggal-snapfb | SNP | ti | HG002compoundhet | hetalt | 97.8831 | 99.8273 | 96.0133 | 26.9417 | 578 | 1 | 578 | 24 | 6 | 25.0000 | |