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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
75151-75200 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 77.8824 | 65.8473 | 95.3008 | 85.1934 | 509 | 264 | 507 | 25 | 6 | 24.0000 | |
| ckim-dragen | SNP | * | map_siren | homalt | 99.7220 | 99.5214 | 99.9236 | 48.9049 | 54892 | 264 | 54896 | 42 | 38 | 90.4762 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.4047 | 93.2256 | 97.6882 | 56.5471 | 3633 | 264 | 3634 | 86 | 79 | 91.8605 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 84.7448 | 77.6461 | 93.2722 | 41.8494 | 917 | 264 | 915 | 66 | 66 | 100.0000 | |
| hfeng-pmm2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 91.4916 | 85.0340 | 99.0106 | 87.6728 | 1500 | 264 | 1501 | 15 | 3 | 20.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | * | het | 99.6628 | 99.6660 | 99.6596 | 60.0640 | 78777 | 264 | 78760 | 269 | 153 | 56.8773 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.0055 | 90.4209 | 93.6466 | 50.9768 | 2492 | 264 | 2491 | 169 | 156 | 92.3077 | |
| anovak-vg | SNP | ti | func_cds | * | 98.6277 | 98.0852 | 99.1763 | 27.7317 | 13523 | 264 | 13486 | 112 | 79 | 70.5357 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 96.1705 | 96.3571 | 95.9846 | 35.8391 | 6983 | 264 | 6980 | 292 | 133 | 45.5479 | |
| ndellapenna-hhga | SNP | * | map_l150_m0_e0 | het | 98.0583 | 96.6751 | 99.4816 | 79.2753 | 7676 | 264 | 7676 | 40 | 17 | 42.5000 | |
| mlin-fermikit | INDEL | I16_PLUS | HG002complexvar | * | 84.0504 | 79.8319 | 88.7395 | 68.1648 | 1045 | 264 | 1056 | 134 | 128 | 95.5224 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.5308 | 95.5496 | 99.5959 | 50.2969 | 5668 | 264 | 5668 | 23 | 21 | 91.3043 | |
| jmaeng-gatk | INDEL | D1_5 | HG002complexvar | * | 99.4486 | 99.1930 | 99.7055 | 58.6476 | 32451 | 264 | 32505 | 96 | 76 | 79.1667 | |
| jli-custom | SNP | ti | map_l125_m1_e0 | * | 99.3574 | 99.1001 | 99.6162 | 66.6526 | 29071 | 264 | 29069 | 112 | 41 | 36.6071 | |
| gduggal-snapplat | INDEL | I1_5 | segdup | * | 78.0848 | 75.0708 | 81.3508 | 96.7377 | 795 | 264 | 807 | 185 | 6 | 3.2432 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 36.0211 | 23.0321 | 82.6087 | 60.0000 | 79 | 264 | 38 | 8 | 8 | 100.0000 | |
| gduggal-snapvard | SNP | tv | map_l125_m2_e1 | het | 90.7385 | 97.4983 | 84.8553 | 82.7554 | 10289 | 264 | 10259 | 1831 | 116 | 6.3353 | |
| ghariani-varprowl | INDEL | * | map_l100_m1_e0 | * | 90.4036 | 92.6380 | 88.2744 | 91.8947 | 3322 | 264 | 3320 | 441 | 203 | 46.0317 | |
| rpoplin-dv42 | SNP | ti | map_l100_m2_e1 | het | 99.3494 | 99.1473 | 99.5523 | 65.6527 | 30696 | 264 | 30688 | 138 | 83 | 60.1449 | |
| rpoplin-dv42 | SNP | tv | HG002complexvar | het | 99.8928 | 99.8249 | 99.9608 | 21.2882 | 150467 | 264 | 150382 | 59 | 46 | 77.9661 | |
| raldana-dualsentieon | SNP | ti | map_l100_m2_e0 | het | 99.0553 | 99.1379 | 98.9728 | 67.5282 | 30358 | 264 | 30351 | 315 | 6 | 1.9048 | |
| raldana-dualsentieon | SNP | ti | map_l100_m2_e1 | het | 99.0592 | 99.1473 | 98.9712 | 67.5574 | 30696 | 264 | 30689 | 319 | 6 | 1.8809 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.8948 | 98.6708 | 99.1198 | 73.7421 | 19598 | 264 | 19594 | 174 | 146 | 83.9080 | |
| mlin-fermikit | INDEL | D1_5 | map_l150_m2_e0 | het | 64.6730 | 48.4436 | 97.2549 | 83.3442 | 249 | 265 | 248 | 7 | 4 | 57.1429 | |
| mlin-fermikit | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.8486 | 98.4572 | 99.2431 | 55.7060 | 16912 | 265 | 16914 | 129 | 121 | 93.7984 | |
| ltrigg-rtg2 | SNP | * | HG002compoundhet | * | 99.3639 | 98.9737 | 99.7572 | 37.9767 | 25557 | 265 | 25473 | 62 | 19 | 30.6452 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 98.0017 | 96.1098 | 99.9695 | 34.1855 | 6547 | 265 | 6563 | 2 | 1 | 50.0000 | |
| hfeng-pmm1 | SNP | * | map_l100_m0_e0 | * | 99.3989 | 99.1931 | 99.6055 | 67.8013 | 32576 | 265 | 32572 | 129 | 37 | 28.6822 | |
| cchapple-custom | SNP | ti | map_l150_m1_e0 | homalt | 98.1515 | 96.3832 | 99.9858 | 66.0349 | 7062 | 265 | 7060 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.6730 | 92.4844 | 99.0893 | 41.0583 | 3261 | 265 | 3808 | 35 | 33 | 94.2857 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.6730 | 92.4844 | 99.0893 | 41.0583 | 3261 | 265 | 3808 | 35 | 33 | 94.2857 | |
| anovak-vg | INDEL | * | map_l150_m2_e0 | het | 71.4142 | 70.7506 | 72.0905 | 91.6109 | 641 | 265 | 669 | 259 | 74 | 28.5714 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 52.4343 | 64.2857 | 44.2724 | 31.6918 | 477 | 265 | 2002 | 2520 | 2292 | 90.9524 | |
| dgrover-gatk | SNP | * | map_l150_m2_e0 | * | 99.1679 | 99.1680 | 99.1679 | 78.4218 | 31587 | 265 | 31581 | 265 | 60 | 22.6415 | |
| dgrover-gatk | SNP | * | map_l150_m2_e1 | * | 99.1741 | 99.1773 | 99.1710 | 78.4616 | 31945 | 265 | 31939 | 267 | 60 | 22.4719 | |
| egarrison-hhga | INDEL | I1_5 | HG002complexvar | het | 98.9830 | 98.5431 | 99.4269 | 55.1160 | 17924 | 265 | 17869 | 103 | 26 | 25.2427 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.6583 | 87.5470 | 98.4034 | 64.1001 | 1863 | 265 | 1849 | 30 | 27 | 90.0000 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.3852 | 95.7925 | 99.0319 | 61.6504 | 6056 | 266 | 6342 | 62 | 53 | 85.4839 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.3852 | 95.7925 | 99.0319 | 61.6504 | 6056 | 266 | 6342 | 62 | 53 | 85.4839 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 35.3557 | 26.5193 | 53.0233 | 64.2263 | 96 | 266 | 114 | 101 | 94 | 93.0693 | |
| ciseli-custom | INDEL | I1_5 | map_l150_m2_e0 | * | 55.9084 | 48.7476 | 65.5352 | 92.4128 | 253 | 266 | 251 | 132 | 111 | 84.0909 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 62.6589 | 45.8248 | 99.0431 | 30.1003 | 225 | 266 | 207 | 2 | 1 | 50.0000 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 62.1803 | 46.4789 | 93.9024 | 80.7963 | 231 | 266 | 231 | 15 | 9 | 60.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 91.5286 | 88.9672 | 94.2418 | 58.4475 | 2145 | 266 | 2144 | 131 | 120 | 91.6031 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.5603 | 90.2098 | 99.3517 | 87.1432 | 2451 | 266 | 2452 | 16 | 4 | 25.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.7089 | 95.5204 | 100.0000 | 63.1123 | 5672 | 266 | 5708 | 0 | 0 | ||
| ckim-vqsr | INDEL | D1_5 | * | het | 99.6940 | 99.6963 | 99.6917 | 60.8657 | 87308 | 266 | 87313 | 270 | 118 | 43.7037 | |
| ckim-isaac | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.5990 | 96.0558 | 99.1926 | 35.3810 | 6478 | 266 | 6511 | 53 | 6 | 11.3208 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 93.9099 | 89.5234 | 98.7484 | 34.7140 | 2273 | 266 | 2288 | 29 | 28 | 96.5517 | |
| egarrison-hhga | SNP | ti | map_l125_m1_e0 | * | 99.4628 | 99.0932 | 99.8351 | 68.9921 | 29069 | 266 | 29069 | 48 | 24 | 50.0000 | |