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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
34101-34150 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | D1_5 | map_l150_m1_e0 | het | 89.8669 | 98.9627 | 82.3024 | 91.9768 | 477 | 5 | 479 | 103 | 4 | 3.8835 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | HG002complexvar | hetalt | 89.8660 | 82.0896 | 99.2701 | 60.2899 | 275 | 60 | 272 | 2 | 2 | 100.0000 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 89.8651 | 88.3469 | 91.4365 | 80.2294 | 326 | 43 | 331 | 31 | 20 | 64.5161 | |
| jlack-gatk | SNP | tv | map_l150_m0_e0 | het | 89.8651 | 98.2765 | 82.7801 | 89.5464 | 2794 | 49 | 2793 | 581 | 34 | 5.8520 | |
| egarrison-hhga | INDEL | D16_PLUS | HG002complexvar | homalt | 89.8612 | 94.8097 | 85.4037 | 66.1053 | 274 | 15 | 275 | 47 | 38 | 80.8511 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 89.8601 | 93.0301 | 86.8990 | 65.5793 | 1268 | 95 | 1247 | 188 | 182 | 96.8085 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 89.8585 | 83.7475 | 96.9315 | 44.2062 | 11527 | 2237 | 3001 | 95 | 94 | 98.9474 | |
| jlack-gatk | INDEL | I1_5 | map_l250_m2_e0 | het | 89.8551 | 93.9394 | 86.1111 | 97.9417 | 62 | 4 | 62 | 10 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I1_5 | map_l250_m2_e1 | het | 89.8551 | 93.9394 | 86.1111 | 98.0083 | 62 | 4 | 62 | 10 | 0 | 0.0000 | |
| ciseli-custom | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 89.8551 | 98.9247 | 82.3088 | 71.2571 | 1748 | 19 | 1754 | 377 | 114 | 30.2387 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 89.8495 | 82.0513 | 99.2857 | 77.1491 | 416 | 91 | 417 | 3 | 2 | 66.6667 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | het | 89.8442 | 86.3636 | 93.6170 | 94.7486 | 57 | 9 | 44 | 3 | 2 | 66.6667 | |
| ltrigg-rtg1 | INDEL | C1_5 | * | het | 89.8401 | 88.8889 | 90.8120 | 96.3931 | 8 | 1 | 425 | 43 | 1 | 2.3256 | |
| gduggal-snapfb | INDEL | * | map_l250_m1_e0 | het | 89.8396 | 88.4211 | 91.3043 | 94.3696 | 168 | 22 | 168 | 16 | 3 | 18.7500 | |
| hfeng-pmm1 | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | * | 89.8396 | 83.1683 | 97.6744 | 93.4799 | 84 | 17 | 84 | 2 | 0 | 0.0000 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 89.8396 | 97.2973 | 83.4437 | 59.6257 | 252 | 7 | 252 | 50 | 48 | 96.0000 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 89.8366 | 96.6865 | 83.8931 | 79.2152 | 2597 | 89 | 2573 | 494 | 7 | 1.4170 | |
| ghariani-varprowl | SNP | * | HG002compoundhet | homalt | 89.8311 | 99.8331 | 81.6508 | 42.6198 | 10764 | 18 | 10773 | 2421 | 2004 | 82.7757 | |
| qzeng-custom | INDEL | * | segdup | hetalt | 89.8305 | 81.5385 | 100.0000 | 96.1039 | 106 | 24 | 24 | 0 | 0 | ||
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 89.8295 | 94.2654 | 85.7923 | 82.5729 | 1726 | 105 | 1727 | 286 | 3 | 1.0490 | |
| asubramanian-gatk | INDEL | D1_5 | map_l125_m2_e0 | het | 89.8280 | 86.6492 | 93.2489 | 90.9553 | 662 | 102 | 663 | 48 | 4 | 8.3333 | |
| gduggal-bwafb | INDEL | D6_15 | func_cds | het | 89.8273 | 89.6552 | 90.0000 | 47.3684 | 26 | 3 | 27 | 3 | 3 | 100.0000 | |
| gduggal-snapplat | SNP | tv | map_l125_m0_e0 | het | 89.8264 | 88.7753 | 90.9027 | 88.4354 | 3907 | 494 | 3907 | 391 | 205 | 52.4297 | |
| astatham-gatk | INDEL | D6_15 | HG002compoundhet | het | 89.8182 | 98.2477 | 82.7210 | 68.4623 | 841 | 15 | 833 | 174 | 172 | 98.8506 | |
| gduggal-bwavard | INDEL | I1_5 | * | * | 89.8158 | 87.7423 | 91.9898 | 54.5219 | 132196 | 18468 | 131206 | 11425 | 10755 | 94.1357 | |
| gduggal-snapvard | INDEL | I1_5 | map_l100_m2_e0 | het | 89.8150 | 98.4868 | 82.5468 | 88.8499 | 781 | 12 | 1102 | 233 | 108 | 46.3519 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m0_e0 | het | 89.8148 | 98.4772 | 82.5532 | 89.6186 | 582 | 9 | 582 | 123 | 22 | 17.8862 | |
| jlack-gatk | INDEL | D6_15 | map_l100_m0_e0 | * | 89.8148 | 94.1748 | 85.8407 | 90.7453 | 97 | 6 | 97 | 16 | 2 | 12.5000 | |
| gduggal-snapvard | INDEL | D1_5 | HG002complexvar | het | 89.8124 | 96.1325 | 84.2721 | 56.4465 | 19960 | 803 | 25510 | 4761 | 3355 | 70.4684 | |
| gduggal-bwaplat | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 89.7995 | 82.2060 | 98.9387 | 71.6625 | 45732 | 9899 | 45775 | 491 | 144 | 29.3279 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 89.7993 | 95.4044 | 84.8163 | 74.1070 | 1038 | 50 | 1039 | 186 | 169 | 90.8602 | |
| gduggal-snapplat | SNP | * | map_l150_m0_e0 | homalt | 89.7981 | 81.5847 | 99.8503 | 78.9397 | 3336 | 753 | 3336 | 5 | 5 | 100.0000 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 89.7973 | 90.4000 | 89.2026 | 69.9879 | 2712 | 288 | 2875 | 348 | 312 | 89.6552 | |
| gduggal-bwavard | INDEL | I1_5 | map_l250_m0_e0 | * | 89.7959 | 91.6667 | 88.0000 | 98.4167 | 22 | 2 | 22 | 3 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 89.7959 | 81.9876 | 99.2481 | 34.4828 | 132 | 29 | 132 | 1 | 1 | 100.0000 | |
| rpoplin-dv42 | INDEL | I16_PLUS | map_l100_m1_e0 | * | 89.7959 | 84.6154 | 95.6522 | 78.3019 | 22 | 4 | 22 | 1 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | I16_PLUS | map_l100_m2_e0 | * | 89.7959 | 84.6154 | 95.6522 | 81.6000 | 22 | 4 | 22 | 1 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | I16_PLUS | map_l100_m2_e1 | * | 89.7959 | 84.6154 | 95.6522 | 81.8898 | 22 | 4 | 22 | 1 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 89.7959 | 100.0000 | 81.4815 | 87.8378 | 22 | 0 | 22 | 5 | 5 | 100.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 89.7959 | 100.0000 | 81.4815 | 87.3832 | 22 | 0 | 22 | 5 | 5 | 100.0000 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 89.7959 | 81.4815 | 100.0000 | 97.5207 | 22 | 5 | 3 | 0 | 0 | ||
| jli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 89.7959 | 91.6667 | 88.0000 | 89.6266 | 22 | 2 | 22 | 3 | 0 | 0.0000 | |
| jli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 89.7959 | 81.4815 | 100.0000 | 90.4762 | 22 | 5 | 18 | 0 | 0 | ||
| jli-custom | INDEL | I16_PLUS | map_l100_m1_e0 | * | 89.7959 | 84.6154 | 95.6522 | 94.0415 | 22 | 4 | 22 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 89.7959 | 81.4815 | 100.0000 | 98.0952 | 22 | 5 | 2 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | I6_15 | map_l125_m1_e0 | * | 89.7959 | 83.0189 | 97.7778 | 90.5263 | 44 | 9 | 44 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | map_l125_m2_e0 | * | 89.7959 | 83.0189 | 97.7778 | 91.7279 | 44 | 9 | 44 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | map_l125_m2_e1 | * | 89.7959 | 83.0189 | 97.7778 | 91.9643 | 44 | 9 | 44 | 1 | 1 | 100.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 89.7959 | 81.4815 | 100.0000 | 98.0952 | 22 | 5 | 2 | 0 | 0 | ||
| ckim-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 89.7959 | 100.0000 | 81.4815 | 87.3832 | 22 | 0 | 22 | 5 | 5 | 100.0000 | |