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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
16601-16650 / 86044 show all | |||||||||||||||
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.7101 | 99.4220 | 100.0000 | 30.6569 | 1720 | 10 | 1710 | 0 | 0 | ||
| asubramanian-gatk | INDEL | I1_5 | HG002complexvar | hetalt | 97.2967 | 95.4229 | 99.2455 | 71.3930 | 1647 | 79 | 1710 | 13 | 11 | 84.6154 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.3028 | 98.7861 | 99.8249 | 33.3463 | 1709 | 21 | 1710 | 3 | 2 | 66.6667 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.5196 | 93.9394 | 99.2455 | 33.2429 | 1519 | 98 | 1710 | 13 | 13 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D1_5 | HG002compoundhet | het | 96.9264 | 96.5856 | 97.2696 | 68.4720 | 1669 | 59 | 1710 | 48 | 21 | 43.7500 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.5196 | 93.9394 | 99.2455 | 33.2429 | 1519 | 98 | 1710 | 13 | 13 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | map_l125_m0_e0 | homalt | 55.1813 | 38.1207 | 99.8832 | 84.5557 | 1712 | 2779 | 1710 | 2 | 2 | 100.0000 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 42.2458 | 32.6120 | 59.9579 | 69.4254 | 1733 | 3581 | 1710 | 1142 | 1085 | 95.0088 | |
| gduggal-bwavard | SNP | ti | map_l250_m2_e1 | homalt | 98.3428 | 97.2348 | 99.4764 | 88.0642 | 1723 | 49 | 1710 | 9 | 6 | 66.6667 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.3024 | 98.7283 | 99.8831 | 33.4500 | 1708 | 22 | 1709 | 2 | 1 | 50.0000 | |
| astatham-gatk | SNP | ti | map_l250_m2_e0 | homalt | 98.7576 | 97.7130 | 99.8248 | 86.3182 | 1709 | 40 | 1709 | 3 | 3 | 100.0000 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 83.1128 | 95.5215 | 73.5573 | 89.2251 | 1685 | 79 | 1708 | 614 | 76 | 12.3779 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 92.9382 | 92.2964 | 93.5890 | 71.7186 | 1258 | 105 | 1708 | 117 | 101 | 86.3248 | |
| jli-custom | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.8328 | 92.0195 | 97.8236 | 63.3039 | 1695 | 147 | 1708 | 38 | 31 | 81.5789 | |
| cchapple-custom | SNP | ti | map_l250_m2_e1 | homalt | 98.1620 | 96.4447 | 99.9415 | 84.8962 | 1709 | 63 | 1708 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 44.4518 | 41.8244 | 47.4313 | 70.0067 | 1701 | 2366 | 1708 | 1893 | 1866 | 98.5737 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 56.5351 | 42.3182 | 85.1372 | 53.5880 | 1705 | 2324 | 1707 | 298 | 259 | 86.9128 | |
| cchapple-custom | SNP | tv | map_l250_m1_e0 | het | 94.4921 | 95.5232 | 93.4830 | 91.0657 | 1707 | 80 | 1707 | 119 | 24 | 20.1681 | |
| jpowers-varprowl | INDEL | D1_5 | map_l100_m1_e0 | * | 93.6112 | 92.3701 | 94.8860 | 83.6796 | 1707 | 141 | 1707 | 92 | 63 | 68.4783 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.3152 | 95.0875 | 99.6497 | 51.5280 | 1684 | 87 | 1707 | 6 | 5 | 83.3333 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 57.0334 | 48.7504 | 68.7072 | 56.9745 | 1736 | 1825 | 1706 | 777 | 550 | 70.7851 | |
| jlack-gatk | SNP | ti | map_l250_m2_e0 | homalt | 98.6412 | 97.5415 | 99.7661 | 86.8218 | 1706 | 43 | 1706 | 4 | 3 | 75.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.5646 | 99.1329 | 100.0000 | 30.3228 | 1715 | 15 | 1705 | 0 | 0 | ||
| ckim-isaac | INDEL | * | map_l100_m2_e0 | het | 84.2881 | 73.9489 | 97.9885 | 86.2255 | 1706 | 601 | 1705 | 35 | 15 | 42.8571 | |
| cchapple-custom | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 24.1656 | 1704 | 0 | 1704 | 0 | 0 | ||
| ckim-dragen | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 26.6781 | 1704 | 0 | 1704 | 0 | 0 | ||
| jlack-gatk | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 25.4919 | 1704 | 0 | 1704 | 0 | 0 | ||
| hfeng-pmm1 | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 25.9774 | 1704 | 0 | 1704 | 0 | 0 | ||
| hfeng-pmm3 | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 26.0096 | 1704 | 0 | 1704 | 0 | 0 | ||
| hfeng-pmm2 | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 25.9774 | 1704 | 0 | 1704 | 0 | 0 | ||
| bgallagher-sentieon | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 24.6018 | 1704 | 0 | 1704 | 0 | 0 | ||
| astatham-gatk | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 24.6351 | 1704 | 0 | 1704 | 0 | 0 | ||
| ltrigg-rtg2 | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 25.7516 | 1704 | 0 | 1704 | 0 | 0 | ||
| ndellapenna-hhga | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 26.5517 | 1704 | 0 | 1704 | 0 | 0 | ||
| gduggal-bwafb | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 28.0101 | 1704 | 0 | 1704 | 0 | 0 | ||
| dgrover-gatk | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 24.6351 | 1704 | 0 | 1704 | 0 | 0 | ||
| egarrison-hhga | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 26.8356 | 1704 | 0 | 1704 | 0 | 0 | ||
| jpowers-varprowl | SNP | tv | func_cds | homalt | 99.8535 | 100.0000 | 99.7074 | 29.3802 | 1704 | 0 | 1704 | 5 | 5 | 100.0000 | |
| jli-custom | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 24.8014 | 1704 | 0 | 1704 | 0 | 0 | ||
| ltrigg-rtg1 | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 26.0096 | 1704 | 0 | 1704 | 0 | 0 | ||
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 51.0900 | 47.6832 | 55.0210 | 72.0588 | 1698 | 1863 | 1704 | 1393 | 1371 | 98.4207 | |
| gduggal-snapfb | SNP | tv | func_cds | homalt | 99.9120 | 100.0000 | 99.8243 | 29.4045 | 1704 | 0 | 1704 | 3 | 0 | 0.0000 | |
| ghariani-varprowl | SNP | tv | func_cds | homalt | 99.7950 | 100.0000 | 99.5909 | 28.7083 | 1704 | 0 | 1704 | 7 | 5 | 71.4286 | |
| raldana-dualsentieon | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 24.3003 | 1704 | 0 | 1704 | 0 | 0 | ||
| rpoplin-dv42 | SNP | tv | func_cds | homalt | 99.9706 | 99.9413 | 100.0000 | 27.8695 | 1703 | 1 | 1703 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | D1_5 | HG002compoundhet | het | 95.8083 | 98.4954 | 93.2640 | 79.3041 | 1702 | 26 | 1703 | 123 | 122 | 99.1870 | |
| ndellapenna-hhga | SNP | tv | map_l250_m1_e0 | het | 97.1755 | 95.2994 | 99.1269 | 86.3845 | 1703 | 84 | 1703 | 15 | 8 | 53.3333 | |
| anovak-vg | INDEL | * | map_l125_m2_e1 | * | 72.6951 | 74.3371 | 71.1241 | 87.8885 | 1654 | 571 | 1702 | 691 | 393 | 56.8741 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 76.1074 | 78.6642 | 73.7116 | 78.2560 | 1696 | 460 | 1702 | 607 | 378 | 62.2735 | |
| dgrover-gatk | INDEL | D1_5 | HG002compoundhet | het | 96.0763 | 98.4375 | 93.8258 | 79.0071 | 1701 | 27 | 1702 | 112 | 111 | 99.1071 | |