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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
6451-6500 / 86044 show all | |||||||||||||||
| gduggal-snapfb | SNP | tv | map_l125_m0_e0 | het | 94.9693 | 96.7280 | 93.2734 | 75.1430 | 4257 | 144 | 4257 | 307 | 123 | 40.0651 | |
| gduggal-snapvard | INDEL | D1_5 | segdup | het | 90.8046 | 97.6879 | 84.8276 | 95.5414 | 676 | 16 | 861 | 154 | 123 | 79.8701 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.9552 | 95.8879 | 96.0225 | 64.6127 | 3078 | 132 | 3066 | 127 | 123 | 96.8504 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.7654 | 99.8573 | 95.7592 | 54.7998 | 2800 | 4 | 2800 | 124 | 123 | 99.1935 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.0003 | 99.8736 | 96.1960 | 56.0166 | 3161 | 4 | 3161 | 125 | 123 | 98.4000 | |
| ciseli-custom | INDEL | I16_PLUS | * | het | 16.1440 | 9.3451 | 59.2506 | 84.8956 | 254 | 2464 | 253 | 174 | 123 | 70.6897 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 77.8716 | 90.2041 | 68.5057 | 80.6495 | 442 | 48 | 298 | 137 | 123 | 89.7810 | |
| anovak-vg | INDEL | D1_5 | map_l100_m2_e1 | * | 84.5768 | 85.6111 | 83.5671 | 84.5427 | 1660 | 279 | 1668 | 328 | 123 | 37.5000 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 34.6434 | 31.9820 | 37.7880 | 55.5328 | 71 | 151 | 82 | 135 | 123 | 91.1111 | |
| eyeh-varpipe | INDEL | * | segdup | * | 93.9572 | 93.0360 | 94.8968 | 96.9158 | 2378 | 178 | 2529 | 136 | 123 | 90.4412 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 93.3528 | 88.7263 | 98.4883 | 45.1727 | 8248 | 1048 | 8535 | 131 | 123 | 93.8931 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 90.9226 | 92.4365 | 89.4575 | 60.7169 | 1491 | 122 | 1451 | 171 | 123 | 71.9298 | |
| egarrison-hhga | INDEL | * | HG002compoundhet | hetalt | 84.8570 | 74.1223 | 99.2275 | 55.5672 | 18664 | 6516 | 18112 | 141 | 123 | 87.2340 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 94.1491 | 90.4125 | 98.2078 | 67.8829 | 13174 | 1397 | 13261 | 242 | 122 | 50.4132 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 94.1491 | 90.4125 | 98.2078 | 67.8829 | 13174 | 1397 | 13261 | 242 | 122 | 50.4132 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 87.2012 | 82.9480 | 91.9141 | 36.2721 | 1435 | 295 | 1455 | 128 | 122 | 95.3125 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.7824 | 99.8573 | 95.7920 | 54.8083 | 2800 | 4 | 2800 | 123 | 122 | 99.1870 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.0155 | 99.8736 | 96.2253 | 56.0241 | 3161 | 4 | 3161 | 124 | 122 | 98.3871 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 89.6491 | 94.3079 | 85.4289 | 76.7105 | 729 | 44 | 727 | 124 | 122 | 98.3871 | |
| ndellapenna-hhga | INDEL | * | HG002compoundhet | hetalt | 85.1313 | 74.5631 | 99.1899 | 56.3007 | 18775 | 6405 | 18000 | 147 | 122 | 82.9932 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 77.4939 | 68.7532 | 88.7808 | 66.4783 | 1329 | 604 | 1369 | 173 | 122 | 70.5202 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 94.3185 | 92.1152 | 96.6299 | 62.4649 | 4895 | 419 | 4903 | 171 | 122 | 71.3450 | |
| gduggal-bwafb | SNP | tv | HG002complexvar | het | 99.7366 | 99.7134 | 99.7598 | 23.4830 | 150302 | 432 | 150365 | 362 | 122 | 33.7017 | |
| jlack-gatk | SNP | ti | HG002complexvar | * | 99.9170 | 99.8944 | 99.9396 | 17.8349 | 507899 | 537 | 507834 | 307 | 122 | 39.7394 | |
| jlack-gatk | SNP | tv | map_siren | * | 97.3060 | 99.4187 | 95.2813 | 67.8334 | 45663 | 267 | 45655 | 2261 | 122 | 5.3958 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 84.7851 | 78.2485 | 92.5134 | 54.4520 | 1644 | 457 | 1557 | 126 | 122 | 96.8254 | |
| raldana-dualsentieon | INDEL | D1_5 | HG002compoundhet | het | 85.6766 | 80.3241 | 91.7935 | 77.7237 | 1388 | 340 | 1387 | 124 | 122 | 98.3871 | |
| anovak-vg | INDEL | D1_5 | map_l100_m2_e0 | * | 84.6007 | 85.6397 | 83.5866 | 84.4811 | 1640 | 275 | 1650 | 324 | 122 | 37.6543 | |
| astatham-gatk | INDEL | D1_5 | * | het | 99.6974 | 99.6803 | 99.7145 | 58.9760 | 87294 | 280 | 87301 | 250 | 122 | 48.8000 | |
| bgallagher-sentieon | INDEL | D1_5 | HG002compoundhet | het | 95.8083 | 98.4954 | 93.2640 | 79.3041 | 1702 | 26 | 1703 | 123 | 122 | 99.1870 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 91.3272 | 98.3182 | 85.2643 | 79.7078 | 760 | 13 | 758 | 131 | 122 | 93.1298 | |
| gduggal-snapfb | SNP | ti | map_l250_m1_e0 | * | 94.3297 | 93.7323 | 94.9347 | 89.2465 | 4292 | 287 | 4292 | 229 | 122 | 53.2751 | |
| gduggal-snapfb | SNP | ti | map_l250_m2_e0 | het | 94.1319 | 95.3903 | 92.9063 | 87.5637 | 3104 | 150 | 3104 | 237 | 122 | 51.4768 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 74.3375 | 67.6709 | 82.4611 | 55.4224 | 584 | 279 | 583 | 124 | 122 | 98.3871 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 75.9768 | 87.8450 | 66.9339 | 67.8314 | 1496 | 207 | 1670 | 825 | 122 | 14.7879 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.0981 | 96.8525 | 99.3761 | 51.0664 | 13324 | 433 | 22937 | 144 | 122 | 84.7222 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.6606 | 99.5951 | 97.7434 | 43.6301 | 5658 | 23 | 5631 | 130 | 122 | 93.8462 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.0981 | 96.8525 | 99.3761 | 51.0664 | 13324 | 433 | 22937 | 144 | 122 | 84.7222 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.5950 | 99.6678 | 97.5451 | 34.2663 | 5100 | 17 | 5086 | 128 | 121 | 94.5312 | |
| jlack-gatk | INDEL | D16_PLUS | HG002compoundhet | het | 80.6922 | 97.5309 | 68.8119 | 59.1507 | 395 | 10 | 278 | 126 | 121 | 96.0317 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.4605 | 98.5514 | 94.4565 | 64.0006 | 2177 | 32 | 2181 | 128 | 121 | 94.5312 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 91.2409 | 95.9430 | 86.9781 | 77.5847 | 875 | 37 | 875 | 131 | 121 | 92.3664 | |
| mlin-fermikit | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.8486 | 98.4572 | 99.2431 | 55.7060 | 16912 | 265 | 16914 | 129 | 121 | 93.7984 | |
| mlin-fermikit | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 98.6888 | 99.4087 | 97.9793 | 56.5956 | 6052 | 36 | 6061 | 125 | 121 | 96.8000 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 85.6106 | 97.3432 | 76.4021 | 67.2751 | 1319 | 36 | 2493 | 770 | 121 | 15.7143 | |
| qzeng-custom | SNP | ti | map_siren | homalt | 93.0187 | 87.2719 | 99.5758 | 47.6263 | 33090 | 4826 | 32626 | 139 | 121 | 87.0504 | |
| ckim-isaac | INDEL | I6_15 | * | homalt | 87.6777 | 79.9968 | 96.9903 | 41.8473 | 4991 | 1248 | 4995 | 155 | 121 | 78.0645 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.3384 | 99.0709 | 97.6165 | 72.3626 | 5545 | 52 | 5529 | 135 | 121 | 89.6296 | |
| jmaeng-gatk | SNP | * | map_siren | * | 94.0415 | 89.7742 | 98.7347 | 67.2383 | 131275 | 14953 | 131252 | 1682 | 121 | 7.1938 | |
| gduggal-bwafb | SNP | * | map_l125_m1_e0 | het | 98.4352 | 98.7039 | 98.1679 | 74.4388 | 28024 | 368 | 28024 | 523 | 121 | 23.1358 | |