PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
7501-7550 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.5254 | 97.4649 | 95.6039 | 64.9385 | 2153 | 56 | 2153 | 99 | 92 | 92.9293 | |
| jlack-gatk | INDEL | D1_5 | HG002complexvar | * | 99.4067 | 99.2878 | 99.5259 | 58.0276 | 32482 | 233 | 32539 | 155 | 92 | 59.3548 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 89.3082 | 97.4828 | 82.3985 | 47.2449 | 426 | 11 | 426 | 91 | 91 | 100.0000 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.4410 | 99.4368 | 95.5239 | 41.0041 | 1942 | 11 | 1942 | 91 | 91 | 100.0000 | |
| jlack-gatk | SNP | tv | map_l125_m2_e1 | * | 95.1831 | 98.8894 | 91.7447 | 81.3088 | 16472 | 185 | 16470 | 1482 | 91 | 6.1404 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.2145 | 93.1450 | 95.3088 | 77.7623 | 2473 | 182 | 2438 | 120 | 91 | 75.8333 | |
| rpoplin-dv42 | SNP | ti | map_l150_m1_e0 | * | 99.1152 | 98.8890 | 99.3424 | 73.3921 | 19493 | 219 | 19489 | 129 | 91 | 70.5426 | |
| dgrover-gatk | INDEL | D16_PLUS | HG002compoundhet | * | 95.7397 | 95.5147 | 95.9657 | 35.4749 | 2236 | 105 | 2236 | 94 | 91 | 96.8085 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 91.7626 | 87.4564 | 96.5147 | 48.4959 | 5013 | 719 | 5040 | 182 | 91 | 50.0000 | |
| gduggal-snapvard | INDEL | D1_5 | map_l125_m1_e0 | het | 85.4186 | 98.2094 | 75.5757 | 89.1583 | 713 | 13 | 919 | 297 | 91 | 30.6397 | |
| gduggal-snapvard | INDEL | D6_15 | map_siren | * | 67.5902 | 64.0472 | 71.5481 | 80.9182 | 326 | 183 | 342 | 136 | 91 | 66.9118 | |
| ghariani-varprowl | SNP | tv | map_l125_m1_e0 | het | 96.7384 | 99.1507 | 94.4408 | 79.1185 | 10040 | 86 | 10040 | 591 | 91 | 15.3976 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 66.9540 | 81.9672 | 56.5891 | 68.9157 | 50 | 11 | 146 | 112 | 91 | 81.2500 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 84.1984 | 77.2530 | 92.5161 | 66.6953 | 1423 | 419 | 1434 | 116 | 91 | 78.4483 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 96.1180 | 95.8000 | 96.4382 | 69.3543 | 2874 | 126 | 2870 | 106 | 91 | 85.8491 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 82.6087 | 95.3668 | 72.8614 | 66.3690 | 247 | 12 | 247 | 92 | 91 | 98.9130 | |
| mlin-fermikit | INDEL | D1_5 | map_l125_m2_e1 | * | 70.7275 | 59.6370 | 86.8852 | 80.8130 | 690 | 467 | 689 | 104 | 91 | 87.5000 | |
| gduggal-bwafb | SNP | * | HG002compoundhet | homalt | 99.2787 | 99.5826 | 98.9767 | 38.6655 | 10737 | 45 | 10736 | 111 | 91 | 81.9820 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 86.3639 | 77.4336 | 97.6228 | 60.1470 | 4399 | 1282 | 4394 | 107 | 91 | 85.0467 | |
| gduggal-bwavard | SNP | ti | map_l150_m1_e0 | * | 95.2687 | 97.5497 | 93.0920 | 81.8831 | 19229 | 483 | 19055 | 1414 | 91 | 6.4356 | |
| anovak-vg | INDEL | I1_5 | map_l125_m0_e0 | homalt | 66.4001 | 91.2281 | 52.1951 | 85.4403 | 104 | 10 | 107 | 98 | 91 | 92.8571 | |
| anovak-vg | INDEL | * | segdup | het | 72.6201 | 63.5061 | 84.7882 | 95.6374 | 931 | 535 | 981 | 176 | 91 | 51.7045 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 43.2760 | 32.9738 | 62.9412 | 68.5185 | 214 | 435 | 214 | 126 | 91 | 72.2222 | |
| jpowers-varprowl | SNP | tv | map_l150_m1_e0 | * | 96.7188 | 96.5726 | 96.8655 | 80.4419 | 10538 | 374 | 10538 | 341 | 91 | 26.6862 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 98.1071 | 96.8411 | 99.4065 | 70.7611 | 14930 | 487 | 15409 | 92 | 91 | 98.9130 | |
| jli-custom | SNP | * | HG002complexvar | * | 99.9396 | 99.9065 | 99.9727 | 19.0201 | 753676 | 705 | 753565 | 206 | 91 | 44.1748 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 92.4301 | 93.6681 | 91.2243 | 68.7320 | 1287 | 87 | 1289 | 124 | 91 | 73.3871 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.9553 | 99.4146 | 96.5382 | 63.5394 | 2717 | 16 | 2705 | 97 | 91 | 93.8144 | |
| cchapple-custom | INDEL | I6_15 | * | het | 98.6365 | 97.9268 | 99.3566 | 49.5505 | 9825 | 208 | 19457 | 126 | 91 | 72.2222 | |
| ckim-dragen | SNP | * | map_l100_m0_e0 | * | 98.2840 | 98.9495 | 97.6275 | 70.9502 | 32496 | 345 | 32508 | 790 | 91 | 11.5190 | |
| ckim-dragen | SNP | * | map_l125_m2_e0 | het | 97.7348 | 98.9665 | 96.5334 | 78.5462 | 29015 | 303 | 29016 | 1042 | 91 | 8.7332 | |
| ckim-dragen | SNP | * | map_l125_m2_e1 | het | 97.7443 | 98.9710 | 96.5476 | 78.6185 | 29335 | 305 | 29336 | 1049 | 91 | 8.6749 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.2782 | 97.1365 | 99.4471 | 33.4959 | 10109 | 298 | 17626 | 98 | 90 | 91.8367 | |
| ciseli-custom | INDEL | * | segdup | het | 88.2244 | 88.4038 | 88.0457 | 95.3251 | 1296 | 170 | 1311 | 178 | 90 | 50.5618 | |
| ciseli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 68.0380 | 93.0844 | 53.6124 | 81.3886 | 6407 | 476 | 6493 | 5618 | 90 | 1.6020 | |
| mlin-fermikit | INDEL | D1_5 | map_l125_m1_e0 | * | 69.1865 | 57.9044 | 85.9290 | 78.9897 | 630 | 458 | 629 | 103 | 90 | 87.3786 | |
| mlin-fermikit | INDEL | D1_5 | map_l125_m2_e0 | * | 70.4052 | 59.2301 | 86.7779 | 80.7464 | 677 | 466 | 676 | 103 | 90 | 87.3786 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 71.9478 | 78.1377 | 66.6667 | 74.2938 | 193 | 54 | 182 | 91 | 90 | 98.9011 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 90.4777 | 92.0158 | 88.9901 | 86.8129 | 1164 | 101 | 1172 | 145 | 90 | 62.0690 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.9374 | 98.0844 | 95.8169 | 84.1185 | 28162 | 550 | 28220 | 1232 | 90 | 7.3052 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.9374 | 98.0844 | 95.8169 | 84.1185 | 28162 | 550 | 28220 | 1232 | 90 | 7.3052 | |
| qzeng-custom | SNP | * | map_l125_m1_e0 | homalt | 83.2331 | 71.6711 | 99.2430 | 64.3421 | 12116 | 4789 | 11930 | 91 | 90 | 98.9011 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 93.7883 | 91.0957 | 96.6448 | 54.7687 | 3550 | 347 | 3543 | 123 | 90 | 73.1707 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 93.1476 | 88.3677 | 98.4741 | 26.6190 | 6085 | 801 | 6260 | 97 | 90 | 92.7835 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.3545 | 97.0864 | 89.8990 | 74.7771 | 933 | 28 | 890 | 100 | 90 | 90.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 78.4352 | 68.5826 | 91.5936 | 64.7059 | 1229 | 563 | 1253 | 115 | 90 | 78.2609 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.8789 | 99.1218 | 96.6667 | 63.6387 | 2709 | 24 | 2697 | 93 | 90 | 96.7742 | |
| jlack-gatk | SNP | tv | map_l100_m1_e0 | het | 94.3447 | 99.3060 | 89.8556 | 80.1334 | 15310 | 107 | 15306 | 1728 | 90 | 5.2083 | |
| jlack-gatk | SNP | tv | map_l100_m2_e0 | het | 94.4020 | 99.3218 | 89.9466 | 81.2769 | 15670 | 107 | 15666 | 1751 | 90 | 5.1399 | |
| jlack-gatk | SNP | tv | map_l100_m2_e1 | het | 94.4530 | 99.3286 | 90.0336 | 81.3037 | 15831 | 107 | 15827 | 1752 | 90 | 5.1370 | |