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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
9451-9500 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0909 | 98.7850 | 99.3987 | 76.0252 | 6342 | 78 | 6282 | 38 | 24 | 63.1579 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 85.8383 | 78.3200 | 94.9533 | 28.7854 | 6340 | 1755 | 2032 | 108 | 63 | 58.3333 | |
| gduggal-snapplat | SNP | tv | map_l150_m1_e0 | het | 91.7565 | 91.2612 | 92.2573 | 87.5714 | 6339 | 607 | 6339 | 532 | 282 | 53.0075 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0437 | 98.7072 | 99.3825 | 75.7366 | 6337 | 83 | 6277 | 39 | 26 | 66.6667 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0437 | 98.7072 | 99.3825 | 75.7366 | 6337 | 83 | 6277 | 39 | 26 | 66.6667 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0359 | 98.7072 | 99.3669 | 75.4765 | 6337 | 83 | 6278 | 40 | 26 | 65.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0359 | 98.7072 | 99.3669 | 75.4765 | 6337 | 83 | 6278 | 40 | 26 | 65.0000 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 94.6117 | 94.0740 | 95.1557 | 42.5447 | 6334 | 399 | 6325 | 322 | 313 | 97.2050 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.0280 | 94.8346 | 99.3253 | 40.5686 | 6334 | 345 | 11482 | 78 | 47 | 60.2564 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.2816 | 94.8346 | 99.8583 | 45.6289 | 6334 | 345 | 6341 | 9 | 7 | 77.7778 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0199 | 98.6449 | 99.3978 | 76.9388 | 6333 | 87 | 6272 | 38 | 24 | 63.1579 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0199 | 98.6449 | 99.3978 | 76.9388 | 6333 | 87 | 6272 | 38 | 24 | 63.1579 | |
| ckim-isaac | SNP | tv | map_l125_m2_e1 | het | 74.8404 | 59.9545 | 99.5595 | 75.8491 | 6327 | 4226 | 6329 | 28 | 7 | 25.0000 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.8861 | 98.5202 | 99.2547 | 76.5663 | 6325 | 95 | 6259 | 47 | 29 | 61.7021 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.8861 | 98.5202 | 99.2547 | 76.5663 | 6325 | 95 | 6259 | 47 | 29 | 61.7021 | |
| astatham-gatk | INDEL | D6_15 | * | homalt | 98.8889 | 99.8893 | 97.9083 | 55.4989 | 6319 | 7 | 6319 | 135 | 133 | 98.5185 | |
| bgallagher-sentieon | INDEL | D6_15 | * | homalt | 98.4421 | 99.8893 | 97.0362 | 55.3606 | 6319 | 7 | 6319 | 193 | 190 | 98.4456 | |
| ckim-gatk | INDEL | D6_15 | * | homalt | 98.8810 | 99.8735 | 97.9079 | 55.6525 | 6318 | 8 | 6318 | 135 | 132 | 97.7778 | |
| raldana-dualsentieon | INDEL | D6_15 | * | homalt | 98.7805 | 99.8735 | 97.7111 | 54.0245 | 6318 | 8 | 6318 | 148 | 145 | 97.9730 | |
| ckim-vqsr | INDEL | D6_15 | * | homalt | 98.8887 | 99.8735 | 97.9231 | 55.6564 | 6318 | 8 | 6318 | 134 | 131 | 97.7612 | |
| dgrover-gatk | INDEL | D6_15 | * | homalt | 98.8732 | 99.8735 | 97.8928 | 55.5601 | 6318 | 8 | 6318 | 136 | 134 | 98.5294 | |
| jmaeng-gatk | INDEL | D6_15 | * | homalt | 98.8031 | 99.8261 | 97.8008 | 55.3272 | 6315 | 11 | 6315 | 142 | 138 | 97.1831 | |
| jmaeng-gatk | SNP | * | map_l150_m1_e0 | homalt | 71.8022 | 56.0188 | 99.9683 | 79.3360 | 6315 | 4958 | 6315 | 2 | 2 | 100.0000 | |
| jli-custom | INDEL | D6_15 | * | homalt | 99.2923 | 99.8103 | 98.7797 | 52.7778 | 6314 | 12 | 6314 | 78 | 76 | 97.4359 | |
| mlin-fermikit | SNP | ti | map_l125_m1_e0 | homalt | 66.1427 | 57.1480 | 78.4977 | 52.8912 | 6312 | 4733 | 6312 | 1729 | 1647 | 95.2574 | |
| ckim-dragen | INDEL | D6_15 | * | homalt | 97.3161 | 99.7471 | 95.0008 | 59.2976 | 6310 | 16 | 6309 | 332 | 329 | 99.0964 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 48.9297 | 42.6581 | 57.3634 | 45.6299 | 6307 | 8478 | 6466 | 4806 | 3764 | 78.3188 | |
| jmaeng-gatk | SNP | tv | map_l100_m1_e0 | homalt | 82.1629 | 69.7335 | 99.9841 | 67.6746 | 6306 | 2737 | 6306 | 1 | 1 | 100.0000 | |
| hfeng-pmm2 | INDEL | D6_15 | * | homalt | 99.3853 | 99.6838 | 99.0886 | 51.6854 | 6306 | 20 | 6306 | 58 | 54 | 93.1034 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.4946 | 98.2087 | 98.7822 | 76.6731 | 6305 | 115 | 6246 | 77 | 38 | 49.3506 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.4946 | 98.2087 | 98.7822 | 76.6731 | 6305 | 115 | 6246 | 77 | 38 | 49.3506 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 0.0000 | 56.7762 | 0.0000 | 0.0000 | 6305 | 4800 | 0 | 0 | 0 | ||
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 82.8968 | 94.7123 | 73.7023 | 85.2096 | 6305 | 352 | 6233 | 2224 | 80 | 3.5971 | |
| cchapple-custom | INDEL | D6_15 | * | homalt | 98.7463 | 99.6364 | 97.8720 | 46.7949 | 6303 | 23 | 6255 | 136 | 133 | 97.7941 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.6890 | 98.1776 | 99.2058 | 77.1478 | 6303 | 117 | 6246 | 50 | 22 | 44.0000 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.6890 | 98.1776 | 99.2058 | 77.1478 | 6303 | 117 | 6246 | 50 | 22 | 44.0000 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 63.5123 | 94.3255 | 47.8735 | 39.2649 | 6300 | 379 | 6281 | 6839 | 6729 | 98.3916 | |
| hfeng-pmm1 | INDEL | D6_15 | * | homalt | 99.4474 | 99.5732 | 99.3220 | 50.6075 | 6299 | 27 | 6299 | 43 | 42 | 97.6744 | |
| jlack-gatk | INDEL | D6_15 | * | homalt | 98.1988 | 99.5416 | 96.8918 | 51.5867 | 6297 | 29 | 6297 | 202 | 199 | 98.5149 | |
| hfeng-pmm3 | INDEL | D6_15 | * | homalt | 99.3845 | 99.5416 | 99.2279 | 50.7795 | 6297 | 29 | 6297 | 49 | 45 | 91.8367 | |
| astatham-gatk | SNP | * | map_l250_m1_e0 | * | 92.7803 | 87.1919 | 99.1341 | 90.2158 | 6297 | 925 | 6297 | 55 | 19 | 34.5455 | |
| ckim-gatk | SNP | tv | map_l100_m1_e0 | homalt | 82.0884 | 69.6340 | 99.9682 | 68.5726 | 6297 | 2746 | 6297 | 2 | 0 | 0.0000 | |
| gduggal-bwaplat | INDEL | D6_15 | HG002compoundhet | * | 81.3435 | 69.7154 | 97.6272 | 45.9650 | 6296 | 2735 | 6295 | 153 | 109 | 71.2418 | |
| anovak-vg | SNP | tv | map_l150_m1_e0 | het | 75.5604 | 90.6277 | 64.7889 | 80.5286 | 6295 | 651 | 6291 | 3419 | 787 | 23.0184 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 95.2271 | 91.4028 | 99.3853 | 26.0145 | 6294 | 592 | 6306 | 39 | 35 | 89.7436 | |
| ckim-gatk | SNP | * | map_l150_m1_e0 | homalt | 71.6189 | 55.8059 | 99.9365 | 80.2510 | 6291 | 4982 | 6291 | 4 | 2 | 50.0000 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5394 | 97.9595 | 99.1262 | 72.9162 | 6289 | 131 | 6239 | 55 | 36 | 65.4545 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5394 | 97.9595 | 99.1262 | 72.9162 | 6289 | 131 | 6239 | 55 | 36 | 65.4545 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5699 | 97.9439 | 99.2039 | 75.0813 | 6288 | 132 | 6231 | 50 | 21 | 42.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5699 | 97.9439 | 99.2039 | 75.0813 | 6288 | 132 | 6231 | 50 | 21 | 42.0000 | |