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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
31301-31350 / 86044 show all | |||||||||||||||
| ckim-gatk | INDEL | D1_5 | HG002complexvar | hetalt | 92.5788 | 88.8314 | 96.6563 | 72.4212 | 1201 | 151 | 1243 | 43 | 43 | 100.0000 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.5787 | 91.0009 | 94.2122 | 75.0968 | 1982 | 196 | 1758 | 108 | 96 | 88.8889 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.5782 | 86.5532 | 99.5046 | 32.0000 | 1577 | 245 | 1607 | 8 | 7 | 87.5000 | |
| eyeh-varpipe | INDEL | * | * | * | 92.5779 | 91.3854 | 93.8021 | 63.3717 | 314861 | 29681 | 317111 | 20953 | 20114 | 95.9958 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 92.5771 | 86.4295 | 99.6662 | 81.9053 | 2089 | 328 | 2090 | 7 | 6 | 85.7143 | |
| rpoplin-dv42 | INDEL | D6_15 | HG002complexvar | hetalt | 92.5754 | 89.1412 | 96.2848 | 45.0369 | 903 | 110 | 933 | 36 | 35 | 97.2222 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.5741 | 90.8365 | 94.3795 | 65.5301 | 1933 | 195 | 2099 | 125 | 115 | 92.0000 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 92.5741 | 90.2916 | 94.9750 | 58.0257 | 14834 | 1595 | 15952 | 844 | 289 | 34.2417 | |
| ckim-isaac | INDEL | D1_5 | HG002compoundhet | hetalt | 92.5735 | 86.7561 | 99.2273 | 35.2319 | 8863 | 1353 | 9117 | 71 | 65 | 91.5493 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 92.5726 | 90.3810 | 94.8730 | 43.3628 | 1945 | 207 | 1943 | 105 | 74 | 70.4762 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.5715 | 90.7713 | 94.4444 | 75.0471 | 1977 | 201 | 1751 | 103 | 93 | 90.2913 | |
| ckim-gatk | INDEL | * | map_l250_m2_e1 | * | 92.5714 | 97.2973 | 88.2834 | 97.3082 | 324 | 9 | 324 | 43 | 4 | 9.3023 | |
| jpowers-varprowl | SNP | tv | map_l250_m2_e0 | het | 92.5700 | 93.7629 | 91.4070 | 92.4193 | 1819 | 121 | 1819 | 171 | 34 | 19.8830 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 92.5656 | 91.5183 | 93.6371 | 69.0667 | 4575 | 424 | 4562 | 310 | 290 | 93.5484 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 92.5656 | 91.5183 | 93.6371 | 69.0667 | 4575 | 424 | 4562 | 310 | 290 | 93.5484 | |
| ciseli-custom | INDEL | D1_5 | segdup | het | 92.5651 | 94.3642 | 90.8333 | 95.6342 | 653 | 39 | 654 | 66 | 21 | 31.8182 | |
| gduggal-bwaplat | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 92.5642 | 86.3306 | 99.7681 | 43.5629 | 3442 | 545 | 3442 | 8 | 8 | 100.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | segdup | * | 92.5620 | 96.5517 | 88.8889 | 96.4467 | 56 | 2 | 56 | 7 | 2 | 28.5714 | |
| asubramanian-gatk | INDEL | D6_15 | map_l100_m0_e0 | het | 92.5620 | 93.3333 | 91.8033 | 92.7467 | 56 | 4 | 56 | 5 | 1 | 20.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | segdup | * | 92.5620 | 96.5517 | 88.8889 | 96.3287 | 56 | 2 | 56 | 7 | 2 | 28.5714 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 92.5616 | 97.8195 | 87.8400 | 82.6726 | 1301 | 29 | 1098 | 152 | 125 | 82.2368 | |
| gduggal-snapvard | INDEL | I1_5 | HG002complexvar | homalt | 92.5606 | 86.5333 | 99.4905 | 33.4524 | 11637 | 1811 | 10935 | 56 | 51 | 91.0714 | |
| jlack-gatk | SNP | ti | map_l250_m0_e0 | * | 92.5591 | 97.1533 | 88.3798 | 95.5349 | 1331 | 39 | 1331 | 175 | 20 | 11.4286 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 92.5582 | 86.9571 | 98.9306 | 27.1355 | 7107 | 1066 | 7308 | 79 | 75 | 94.9367 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 92.5569 | 94.9365 | 90.2936 | 47.5778 | 11887 | 634 | 11256 | 1210 | 1034 | 85.4545 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.5568 | 89.9466 | 95.3230 | 44.4415 | 3534 | 395 | 3954 | 194 | 181 | 93.2990 | |
| anovak-vg | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 92.5559 | 94.4948 | 90.6950 | 66.9104 | 2918 | 170 | 3119 | 320 | 136 | 42.5000 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 92.5554 | 89.9881 | 95.2735 | 38.7245 | 28789 | 3203 | 28422 | 1410 | 1207 | 85.6028 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 92.5543 | 91.9137 | 93.2039 | 71.7808 | 682 | 60 | 672 | 49 | 46 | 93.8776 | |
| ckim-vqsr | INDEL | D1_5 | map_l250_m2_e0 | * | 92.5532 | 94.5652 | 90.6250 | 97.1080 | 174 | 10 | 174 | 18 | 1 | 5.5556 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.5450 | 87.1936 | 98.5962 | 31.1755 | 2063 | 303 | 2107 | 30 | 29 | 96.6667 | |
| jlack-gatk | SNP | * | map_l125_m0_e0 | het | 92.5432 | 98.6576 | 87.1425 | 85.9677 | 12494 | 170 | 12491 | 1843 | 134 | 7.2708 | |
| qzeng-custom | SNP | ti | map_siren | * | 92.5421 | 86.8188 | 99.0732 | 61.8902 | 87127 | 13228 | 86370 | 808 | 570 | 70.5446 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 92.5413 | 96.7290 | 88.7011 | 66.3212 | 3519 | 119 | 3517 | 448 | 445 | 99.3304 | |
| ghariani-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 92.5410 | 98.7028 | 87.1034 | 79.6250 | 30739 | 404 | 30832 | 4565 | 319 | 6.9880 | |
| ghariani-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 92.5410 | 98.7028 | 87.1034 | 79.6250 | 30739 | 404 | 30832 | 4565 | 319 | 6.9880 | |
| qzeng-custom | INDEL | D6_15 | * | het | 92.5374 | 97.5155 | 88.0429 | 52.4636 | 11304 | 288 | 19299 | 2621 | 996 | 38.0008 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l250_m0_e0 | het | 92.5373 | 93.9394 | 91.1765 | 96.9479 | 31 | 2 | 31 | 3 | 1 | 33.3333 | |
| cchapple-custom | INDEL | D1_5 | map_l250_m0_e0 | het | 92.5373 | 93.9394 | 91.1765 | 97.1878 | 31 | 2 | 31 | 3 | 0 | 0.0000 | |
| jpowers-varprowl | INDEL | D1_5 | map_l250_m1_e0 | * | 92.5373 | 90.6433 | 94.5122 | 95.5544 | 155 | 16 | 155 | 9 | 4 | 44.4444 | |
| egarrison-hhga | INDEL | D1_5 | map_l250_m0_e0 | het | 92.5373 | 93.9394 | 91.1765 | 97.2313 | 31 | 2 | 31 | 3 | 1 | 33.3333 | |
| astatham-gatk | SNP | ti | map_l100_m0_e0 | * | 92.5350 | 86.2891 | 99.7557 | 72.1287 | 18786 | 2985 | 18783 | 46 | 24 | 52.1739 | |
| eyeh-varpipe | INDEL | * | * | homalt | 92.5348 | 96.0734 | 89.2476 | 55.4307 | 120257 | 4915 | 121109 | 14591 | 14265 | 97.7657 | |
| eyeh-varpipe | SNP | tv | HG002compoundhet | het | 92.5346 | 98.5876 | 87.1819 | 61.1401 | 4607 | 66 | 1884 | 277 | 44 | 15.8845 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m2_e0 | het | 92.5331 | 98.8057 | 87.0093 | 88.9275 | 1241 | 15 | 1219 | 182 | 48 | 26.3736 | |
| hfeng-pmm1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.5301 | 86.8778 | 98.9691 | 90.9683 | 192 | 29 | 192 | 2 | 0 | 0.0000 | |
| ckim-gatk | INDEL | * | map_l250_m2_e0 | * | 92.5287 | 97.2810 | 88.2192 | 97.2498 | 322 | 9 | 322 | 43 | 4 | 9.3023 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 92.5252 | 93.1034 | 91.9540 | 99.8905 | 81 | 6 | 80 | 7 | 0 | 0.0000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 92.5242 | 92.9345 | 92.1175 | 55.9701 | 12785 | 972 | 12446 | 1065 | 828 | 77.7465 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 92.5242 | 92.9345 | 92.1175 | 55.9701 | 12785 | 972 | 12446 | 1065 | 828 | 77.7465 | |