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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
8001-8050 / 86044 show all | |||||||||||||||
| qzeng-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 90.2766 | 96.5517 | 84.7674 | 66.2145 | 588 | 21 | 1330 | 239 | 80 | 33.4728 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 79.4289 | 78.4553 | 80.4270 | 61.9241 | 193 | 53 | 678 | 165 | 80 | 48.4848 | |
| ltrigg-rtg2 | INDEL | D1_5 | HG002compoundhet | * | 97.8414 | 96.6244 | 99.0893 | 63.2729 | 11822 | 413 | 11860 | 109 | 80 | 73.3945 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.1456 | 97.0290 | 99.2882 | 49.3199 | 17146 | 525 | 17018 | 122 | 80 | 65.5738 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.1456 | 97.0290 | 99.2882 | 49.3199 | 17146 | 525 | 17018 | 122 | 80 | 65.5738 | |
| dgrover-gatk | INDEL | I16_PLUS | * | * | 97.6461 | 96.9265 | 98.3766 | 71.1206 | 6181 | 196 | 6181 | 102 | 80 | 78.4314 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.2070 | 98.3037 | 98.1104 | 53.8870 | 5969 | 103 | 5971 | 115 | 80 | 69.5652 | |
| egarrison-hhga | SNP | ti | * | het | 99.8877 | 99.8228 | 99.9527 | 17.2025 | 1279619 | 2272 | 1279622 | 606 | 80 | 13.2013 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 93.4325 | 88.9626 | 98.3752 | 33.8873 | 6569 | 815 | 6418 | 106 | 80 | 75.4717 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.8975 | 95.7372 | 96.0584 | 69.6019 | 4649 | 207 | 4606 | 189 | 80 | 42.3280 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 68.0328 | 54.2991 | 91.0658 | 88.7322 | 3486 | 2934 | 3486 | 342 | 80 | 23.3918 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 68.0328 | 54.2991 | 91.0658 | 88.7322 | 3486 | 2934 | 3486 | 342 | 80 | 23.3918 | |
| gduggal-bwaplat | SNP | * | map_l100_m1_e0 | het | 86.2179 | 76.2737 | 99.1438 | 83.9192 | 34597 | 10762 | 34621 | 299 | 80 | 26.7559 | |
| gduggal-bwafb | SNP | tv | map_siren | * | 99.0828 | 99.3686 | 98.7986 | 61.3728 | 45640 | 290 | 45640 | 555 | 80 | 14.4144 | |
| gduggal-bwafb | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.5802 | 99.1091 | 98.0569 | 48.2748 | 18021 | 162 | 18066 | 358 | 80 | 22.3464 | |
| gduggal-bwafb | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.0758 | 97.7052 | 94.4998 | 74.6425 | 4726 | 111 | 4742 | 276 | 80 | 28.9855 | |
| jmaeng-gatk | SNP | tv | * | * | 99.5370 | 99.3842 | 99.6902 | 27.5023 | 963719 | 5971 | 963632 | 2995 | 80 | 2.6711 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 45.6818 | 35.2014 | 65.0485 | 65.2418 | 201 | 370 | 201 | 108 | 80 | 74.0741 | |
| ltrigg-rtg1 | SNP | ti | HG002complexvar | * | 99.8532 | 99.7400 | 99.9667 | 17.5108 | 507114 | 1322 | 507034 | 169 | 80 | 47.3373 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.4223 | 99.8206 | 99.0272 | 61.0885 | 8345 | 15 | 8347 | 82 | 80 | 97.5610 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.4223 | 99.8206 | 99.0272 | 61.0885 | 8345 | 15 | 8347 | 82 | 80 | 97.5610 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.0007 | 98.1907 | 97.8114 | 63.8674 | 3799 | 70 | 3754 | 84 | 80 | 95.2381 | |
| ckim-dragen | SNP | * | * | homalt | 99.9725 | 99.9534 | 99.9917 | 17.1093 | 1179611 | 550 | 1179821 | 98 | 80 | 81.6327 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.9600 | 91.6530 | 96.3860 | 42.0652 | 560 | 51 | 2347 | 88 | 80 | 90.9091 | |
| ciseli-custom | INDEL | D1_5 | segdup | * | 89.4589 | 90.6618 | 88.2875 | 95.2028 | 1000 | 103 | 995 | 132 | 80 | 60.6061 | |
| ckim-dragen | SNP | tv | HG002complexvar | * | 99.9267 | 99.9175 | 99.9359 | 22.5633 | 245949 | 203 | 246200 | 158 | 80 | 50.6329 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 92.2388 | 86.5886 | 98.6779 | 34.8864 | 7244 | 1122 | 7240 | 97 | 80 | 82.4742 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 59.4331 | 51.2295 | 70.7650 | 59.7360 | 250 | 238 | 259 | 107 | 80 | 74.7664 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 78.7119 | 72.4534 | 86.1538 | 53.4606 | 505 | 192 | 504 | 81 | 80 | 98.7654 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 67.7132 | 76.4249 | 60.7843 | 87.7538 | 295 | 91 | 341 | 220 | 80 | 36.3636 | |
| anovak-vg | SNP | tv | segdup | * | 97.7325 | 97.6676 | 97.7974 | 93.3295 | 8333 | 199 | 8303 | 187 | 80 | 42.7807 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.3586 | 98.2333 | 98.4842 | 57.4113 | 6561 | 118 | 6562 | 101 | 80 | 79.2079 | |
| jlack-gatk | SNP | tv | map_l125_m1_e0 | het | 92.8605 | 99.0519 | 87.3976 | 83.4310 | 10030 | 96 | 10028 | 1446 | 80 | 5.5325 | |
| 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 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 64.2536 | 98.2249 | 47.7419 | 79.1667 | 166 | 3 | 74 | 81 | 79 | 97.5309 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.4122 | 99.6041 | 99.2209 | 44.4011 | 10316 | 41 | 10316 | 81 | 79 | 97.5309 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.2950 | 93.8423 | 98.8793 | 50.2372 | 7879 | 517 | 13588 | 154 | 79 | 51.2987 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 77.2155 | 68.0091 | 89.3048 | 56.7130 | 2398 | 1128 | 668 | 80 | 79 | 98.7500 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 77.2155 | 68.0091 | 89.3048 | 56.7130 | 2398 | 1128 | 668 | 80 | 79 | 98.7500 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 94.8865 | 95.8225 | 93.9686 | 74.8872 | 2959 | 129 | 2929 | 188 | 79 | 42.0213 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 60.3325 | 43.6538 | 97.6360 | 47.3850 | 3006 | 3880 | 3428 | 83 | 79 | 95.1807 | |
| gduggal-bwafb | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.4793 | 99.5219 | 97.4583 | 69.5878 | 17484 | 84 | 17523 | 457 | 79 | 17.2867 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 86.1301 | 82.0915 | 90.5865 | 80.5712 | 1256 | 274 | 1251 | 130 | 79 | 60.7692 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 86.1301 | 82.0915 | 90.5865 | 80.5712 | 1256 | 274 | 1251 | 130 | 79 | 60.7692 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 92.3787 | 95.5903 | 89.3758 | 38.2787 | 672 | 31 | 673 | 80 | 79 | 98.7500 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 90.7728 | 88.5693 | 93.0888 | 46.5749 | 1170 | 151 | 3071 | 228 | 79 | 34.6491 | |
| ndellapenna-hhga | SNP | * | HG002complexvar | het | 99.7473 | 99.5353 | 99.9601 | 18.3091 | 463334 | 2163 | 463353 | 185 | 79 | 42.7027 | |
| ghariani-varprowl | INDEL | * | map_l125_m2_e0 | * | 91.8919 | 94.4444 | 89.4737 | 94.0645 | 2074 | 122 | 2074 | 244 | 79 | 32.3770 | |
| ghariani-varprowl | SNP | ti | map_l150_m0_e0 | het | 96.0700 | 98.0773 | 94.1431 | 85.9691 | 4999 | 98 | 4999 | 311 | 79 | 25.4019 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 83.0586 | 77.6471 | 89.2809 | 34.5471 | 660 | 190 | 658 | 79 | 79 | 100.0000 | |