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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
21201-21250 / 86044 show all | |||||||||||||||
| gduggal-snapplat | SNP | tv | HG002complexvar | * | 97.5342 | 96.7281 | 98.3538 | 26.8142 | 238101 | 8054 | 238450 | 3991 | 673 | 16.8629 | |
| ciseli-custom | SNP | tv | func_cds | homalt | 99.1797 | 99.8826 | 98.4866 | 26.8313 | 1702 | 2 | 1692 | 26 | 9 | 34.6154 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.2695 | 92.8074 | 100.0000 | 26.8341 | 6658 | 516 | 6702 | 0 | 0 | ||
| egarrison-hhga | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 26.8356 | 1704 | 0 | 1704 | 0 | 0 | ||
| qzeng-custom | INDEL | I6_15 | HG002compoundhet | hetalt | 81.2263 | 68.6424 | 99.4598 | 26.8379 | 5860 | 2677 | 3682 | 20 | 14 | 70.0000 | |
| asubramanian-gatk | SNP | * | HG002compoundhet | hetalt | 95.0437 | 94.5476 | 95.5451 | 26.8439 | 815 | 47 | 815 | 38 | 0 | 0.0000 | |
| astatham-gatk | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.9650 | 100.0000 | 99.9300 | 26.8443 | 1427 | 0 | 1427 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.8949 | 99.9299 | 99.8599 | 26.8443 | 1426 | 1 | 1426 | 2 | 2 | 100.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.3658 | 98.8087 | 99.9291 | 26.8533 | 1410 | 17 | 1410 | 1 | 1 | 100.0000 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 79.6057 | 84.7414 | 75.0569 | 26.8642 | 1655 | 298 | 1649 | 548 | 546 | 99.6350 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 94.2777 | 89.5819 | 99.4931 | 26.8704 | 6492 | 755 | 6477 | 33 | 25 | 75.7576 | |
| gduggal-snapplat | SNP | * | * | * | 99.0030 | 98.6815 | 99.3266 | 26.8746 | 3014360 | 40274 | 3015151 | 20442 | 2819 | 13.7902 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.6815 | 93.6024 | 99.9702 | 26.8790 | 6657 | 455 | 6701 | 2 | 1 | 50.0000 | |
| raldana-dualsentieon | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.9650 | 100.0000 | 99.9300 | 26.8817 | 1427 | 0 | 1427 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 70.4512 | 54.9658 | 98.0843 | 26.8908 | 321 | 263 | 256 | 5 | 4 | 80.0000 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 68.1056 | 52.0548 | 98.4674 | 26.8908 | 304 | 280 | 257 | 4 | 4 | 100.0000 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.9353 | 96.3590 | 99.5640 | 26.8986 | 5240 | 198 | 5252 | 23 | 22 | 95.6522 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.8836 | 92.6404 | 99.3621 | 26.9063 | 4305 | 342 | 4829 | 31 | 30 | 96.7742 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 85.1335 | 74.1972 | 99.8510 | 26.9063 | 647 | 225 | 670 | 1 | 1 | 100.0000 | |
| gduggal-snapvard | INDEL | I6_15 | HG002complexvar | homalt | 45.0525 | 29.6785 | 93.4732 | 26.9165 | 360 | 853 | 401 | 28 | 27 | 96.4286 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 54.1237 | 72.0257 | 43.3492 | 26.9375 | 224 | 87 | 1271 | 1661 | 1654 | 99.5786 | |
| gduggal-snapfb | SNP | ti | HG002compoundhet | hetalt | 97.8831 | 99.8273 | 96.0133 | 26.9417 | 578 | 1 | 578 | 24 | 6 | 25.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 97.9592 | 96.0000 | 100.0000 | 26.9461 | 120 | 5 | 122 | 0 | 0 | ||
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 97.9592 | 96.0000 | 100.0000 | 26.9461 | 120 | 5 | 122 | 0 | 0 | ||
| cchapple-custom | SNP | tv | * | het | 99.6701 | 99.8702 | 99.4708 | 26.9512 | 590928 | 768 | 591553 | 3147 | 233 | 7.4039 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 97.5795 | 95.7485 | 99.4819 | 26.9554 | 6869 | 305 | 6912 | 36 | 34 | 94.4444 | |
| ckim-vqsr | SNP | * | * | het | 99.4736 | 99.0611 | 99.8894 | 26.9578 | 1855996 | 17591 | 1855876 | 2054 | 101 | 4.9172 | |
| ghariani-varprowl | SNP | tv | HG002complexvar | het | 98.7696 | 99.5137 | 98.0366 | 26.9661 | 149998 | 733 | 150145 | 3007 | 54 | 1.7958 | |
| dgrover-gatk | SNP | * | func_cds | het | 99.8970 | 99.9642 | 99.8299 | 26.9739 | 11157 | 4 | 11154 | 19 | 0 | 0.0000 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.2901 | 93.2087 | 99.5822 | 26.9805 | 6629 | 483 | 6673 | 28 | 28 | 100.0000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 96.8421 | 93.8776 | 100.0000 | 26.9841 | 46 | 3 | 46 | 0 | 0 | ||
| bgallagher-sentieon | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.9650 | 100.0000 | 99.9300 | 26.9939 | 1427 | 0 | 1427 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.3146 | 92.8912 | 100.0000 | 26.9952 | 7592 | 581 | 7629 | 0 | 0 | ||
| anovak-vg | INDEL | D16_PLUS | HG002compoundhet | het | 47.7497 | 45.4321 | 50.3165 | 27.0208 | 184 | 221 | 477 | 471 | 319 | 67.7282 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 72.7273 | 57.1429 | 100.0000 | 27.0270 | 28 | 21 | 27 | 0 | 0 | ||
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 85.5100 | 74.7706 | 99.8519 | 27.0270 | 652 | 220 | 674 | 1 | 1 | 100.0000 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.8922 | 94.2909 | 99.6412 | 27.0291 | 10471 | 634 | 10553 | 38 | 38 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.8827 | 94.2729 | 99.6411 | 27.0328 | 10469 | 636 | 10551 | 38 | 38 | 100.0000 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 99.1898 | 98.3926 | 100.0000 | 27.0507 | 1163 | 19 | 1165 | 0 | 0 | ||
| gduggal-bwaplat | SNP | tv | func_cds | homalt | 99.4394 | 98.8850 | 100.0000 | 27.0563 | 1685 | 19 | 1685 | 0 | 0 | ||
| ltrigg-rtg1 | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.6975 | 99.6368 | 99.7584 | 27.0564 | 2469 | 9 | 2477 | 6 | 0 | 0.0000 | |
| cchapple-custom | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.7987 | 99.5982 | 100.0000 | 27.0777 | 2727 | 11 | 2720 | 0 | 0 | ||
| asubramanian-gatk | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.3658 | 98.8087 | 99.9291 | 27.0801 | 1410 | 17 | 1410 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | * | * | het | 99.5639 | 99.9321 | 99.1985 | 27.0831 | 1872315 | 1272 | 1872190 | 15127 | 441 | 2.9153 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 63.3484 | 46.3576 | 100.0000 | 27.0833 | 70 | 81 | 70 | 0 | 0 | ||
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.7497 | 95.9658 | 99.6012 | 27.0945 | 10657 | 448 | 10739 | 43 | 42 | 97.6744 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 98.2940 | 96.7497 | 99.8884 | 27.0952 | 893 | 30 | 895 | 1 | 1 | 100.0000 | |
| jli-custom | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.9650 | 100.0000 | 99.9300 | 27.1057 | 1427 | 0 | 1427 | 1 | 1 | 100.0000 | |
| dgrover-gatk | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.9650 | 100.0000 | 99.9300 | 27.1057 | 1427 | 0 | 1427 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 98.2699 | 96.6164 | 99.9810 | 27.1104 | 5254 | 184 | 5266 | 1 | 0 | 0.0000 | |