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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
48851-48900 / 86044 show all | |||||||||||||||
| ckim-dragen | INDEL | * | map_l100_m0_e0 | het | 95.6303 | 96.7679 | 94.5192 | 88.5902 | 988 | 33 | 983 | 57 | 4 | 7.0175 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 84.5429 | 76.4706 | 94.5205 | 47.1014 | 65 | 20 | 69 | 4 | 2 | 50.0000 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 89.9659 | 85.8300 | 94.5205 | 76.9716 | 212 | 35 | 207 | 12 | 8 | 66.6667 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 93.2432 | 92.0000 | 94.5205 | 64.5631 | 69 | 6 | 69 | 4 | 3 | 75.0000 | |
| ndellapenna-hhga | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 79.5193 | 68.6275 | 94.5205 | 91.5704 | 70 | 32 | 69 | 4 | 3 | 75.0000 | |
| ckim-gatk | INDEL | I1_5 | segdup | het | 96.8319 | 99.2565 | 94.5230 | 96.6704 | 534 | 4 | 535 | 31 | 0 | 0.0000 | |
| ghariani-varprowl | SNP | * | segdup | het | 96.9575 | 99.5207 | 94.5230 | 93.2841 | 17234 | 83 | 17241 | 999 | 5 | 0.5005 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 96.9475 | 99.4987 | 94.5238 | 65.8537 | 397 | 2 | 397 | 23 | 23 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 86.6576 | 80.0000 | 94.5238 | 69.3431 | 392 | 98 | 397 | 23 | 21 | 91.3043 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 96.5231 | 98.6023 | 94.5298 | 62.0425 | 12346 | 175 | 12304 | 712 | 693 | 97.3315 | |
| gduggal-snapvard | SNP | ti | map_siren | het | 95.3627 | 96.2088 | 94.5314 | 68.3335 | 60017 | 2365 | 59499 | 3442 | 355 | 10.3138 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 94.9278 | 95.3271 | 94.5317 | 83.5556 | 1734 | 85 | 1504 | 87 | 55 | 63.2184 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 94.9278 | 95.3271 | 94.5317 | 83.5556 | 1734 | 85 | 1504 | 87 | 55 | 63.2184 | |
| ndellapenna-hhga | INDEL | I16_PLUS | HG002complexvar | homalt | 94.6777 | 94.8220 | 94.5338 | 66.1957 | 293 | 16 | 294 | 17 | 10 | 58.8235 | |
| ghariani-varprowl | SNP | tv | map_l125_m0_e0 | * | 96.2771 | 98.0848 | 94.5349 | 81.3241 | 6504 | 127 | 6504 | 376 | 68 | 18.0851 | |
| cchapple-custom | SNP | tv | map_l100_m1_e0 | het | 96.2530 | 98.0346 | 94.5349 | 73.9009 | 15114 | 303 | 15153 | 876 | 133 | 15.1826 | |
| bgallagher-sentieon | INDEL | I16_PLUS | * | homalt | 97.0698 | 99.7438 | 94.5355 | 72.0279 | 1557 | 4 | 1557 | 90 | 87 | 96.6667 | |
| ckim-gatk | INDEL | * | segdup | het | 96.8043 | 99.1814 | 94.5384 | 96.5594 | 1454 | 12 | 1454 | 84 | 1 | 1.1905 | |
| eyeh-varpipe | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.5573 | 98.6641 | 94.5386 | 64.0244 | 517 | 7 | 502 | 29 | 9 | 31.0345 | |
| gduggal-snapfb | INDEL | I1_5 | map_l100_m2_e1 | het | 95.1055 | 95.6790 | 94.5388 | 84.7999 | 775 | 35 | 779 | 45 | 6 | 13.3333 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 91.0608 | 87.8273 | 94.5415 | 37.6092 | 12107 | 1678 | 12020 | 694 | 633 | 91.2104 | |
| ciseli-custom | SNP | tv | * | * | 96.5740 | 98.6920 | 94.5451 | 25.2127 | 957014 | 12684 | 954909 | 55095 | 4019 | 7.2947 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 72.8872 | 59.3023 | 94.5455 | 73.4300 | 51 | 35 | 52 | 3 | 2 | 66.6667 | |
| gduggal-snapfb | INDEL | I1_5 | map_l125_m1_e0 | het | 95.1089 | 95.6790 | 94.5455 | 85.1619 | 465 | 21 | 468 | 27 | 3 | 11.1111 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.2414 | 93.9394 | 94.5455 | 90.9836 | 155 | 10 | 156 | 9 | 2 | 22.2222 | |
| ndellapenna-hhga | INDEL | D6_15 | HG002complexvar | hetalt | 66.5397 | 51.3327 | 94.5493 | 59.4388 | 520 | 493 | 451 | 26 | 23 | 88.4615 | |
| gduggal-snapfb | SNP | tv | map_l250_m1_e0 | * | 94.8003 | 95.0510 | 94.5509 | 89.8505 | 2516 | 131 | 2516 | 145 | 53 | 36.5517 | |
| ciseli-custom | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 96.0994 | 97.6994 | 94.5510 | 57.2127 | 10829 | 255 | 10845 | 625 | 21 | 3.3600 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.2480 | 98.0066 | 94.5513 | 51.4774 | 590 | 12 | 590 | 34 | 33 | 97.0588 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 91.3518 | 88.3601 | 94.5531 | 56.1456 | 1708 | 225 | 1788 | 103 | 103 | 100.0000 | |
| gduggal-bwavard | SNP | ti | map_l125_m1_e0 | * | 95.9902 | 97.4706 | 94.5540 | 78.3647 | 28593 | 742 | 28335 | 1632 | 115 | 7.0466 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 95.5259 | 96.5174 | 94.5545 | 88.5617 | 194 | 7 | 191 | 11 | 2 | 18.1818 | |
| jpowers-varprowl | INDEL | * | map_l125_m2_e1 | * | 92.9861 | 91.4607 | 94.5632 | 88.4195 | 2035 | 190 | 2035 | 117 | 81 | 69.2308 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 79.0248 | 67.8719 | 94.5637 | 68.1984 | 657 | 311 | 661 | 38 | 8 | 21.0526 | |
| gduggal-bwavard | INDEL | C6_15 | * | homalt | 0.0000 | 0.0000 | 94.5652 | 91.2130 | 0 | 0 | 87 | 5 | 2 | 40.0000 | |
| gduggal-bwavard | INDEL | C6_15 | HG002complexvar | homalt | 0.0000 | 0.0000 | 94.5652 | 79.6460 | 0 | 0 | 87 | 5 | 2 | 40.0000 | |
| gduggal-snapfb | INDEL | D6_15 | map_l100_m1_e0 | * | 77.1252 | 65.1163 | 94.5652 | 81.3576 | 168 | 90 | 174 | 10 | 9 | 90.0000 | |
| cchapple-custom | INDEL | I16_PLUS | map_siren | * | 96.0947 | 97.6744 | 94.5652 | 91.4736 | 84 | 2 | 87 | 5 | 2 | 40.0000 | |
| gduggal-snapfb | SNP | * | map_l150_m1_e0 | het | 95.7011 | 96.8575 | 94.5719 | 74.7840 | 18709 | 607 | 18712 | 1074 | 507 | 47.2067 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 94.5830 | 94.5931 | 94.5728 | 62.5553 | 1732 | 99 | 1760 | 101 | 45 | 44.5545 | |
| cchapple-custom | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.2112 | 100.0000 | 94.5736 | 84.5324 | 122 | 0 | 122 | 7 | 7 | 100.0000 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 92.9356 | 91.3534 | 94.5736 | 81.3987 | 243 | 23 | 244 | 14 | 11 | 78.5714 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.8586 | 99.2554 | 94.5749 | 83.0098 | 9065 | 68 | 9065 | 520 | 22 | 4.2308 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.8586 | 99.2554 | 94.5749 | 83.0098 | 9065 | 68 | 9065 | 520 | 22 | 4.2308 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 82.0159 | 72.4008 | 94.5759 | 92.8167 | 1915 | 730 | 1918 | 110 | 13 | 11.8182 | |
| jlack-gatk | INDEL | D6_15 | * | het | 96.7124 | 98.9476 | 94.5760 | 63.3561 | 11470 | 122 | 11421 | 655 | 345 | 52.6718 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.6969 | 92.8325 | 94.5775 | 63.9536 | 5647 | 436 | 5529 | 317 | 301 | 94.9527 | |
| asubramanian-gatk | INDEL | I1_5 | map_l150_m0_e0 | * | 91.8129 | 89.2045 | 94.5783 | 94.1487 | 157 | 19 | 157 | 9 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.5222 | 92.4891 | 94.5785 | 50.7408 | 2549 | 207 | 2547 | 146 | 141 | 96.5753 | |
| qzeng-custom | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.6977 | 98.9130 | 94.5794 | 80.5719 | 2002 | 22 | 2024 | 116 | 6 | 5.1724 | |