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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
9101-9150 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 83.2650 | 74.7927 | 93.9018 | 56.7791 | 1804 | 608 | 1817 | 118 | 62 | 52.5424 | |
| gduggal-bwaplat | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 64.8666 | 51.1386 | 88.6695 | 86.4061 | 2066 | 1974 | 2066 | 264 | 62 | 23.4848 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 89.1252 | 99.3103 | 80.8349 | 77.3820 | 432 | 3 | 426 | 101 | 62 | 61.3861 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 88.7892 | 84.1909 | 93.9189 | 55.0542 | 2258 | 424 | 973 | 63 | 62 | 98.4127 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 59.5793 | 42.8121 | 97.9353 | 47.2358 | 1629 | 2176 | 3178 | 67 | 62 | 92.5373 | |
| jpowers-varprowl | INDEL | D1_5 | map_l100_m2_e1 | het | 94.4493 | 95.8991 | 93.0428 | 86.2663 | 1216 | 52 | 1217 | 91 | 62 | 68.1319 | |
| jli-custom | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 96.1711 | 94.2520 | 98.1699 | 58.1784 | 3755 | 229 | 3755 | 70 | 62 | 88.5714 | |
| ltrigg-rtg1 | INDEL | * | HG002compoundhet | het | 96.0922 | 95.0904 | 97.1154 | 68.4751 | 3893 | 201 | 3939 | 117 | 62 | 52.9915 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.4824 | 95.5531 | 99.4912 | 43.7067 | 13172 | 613 | 13100 | 67 | 62 | 92.5373 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 81.2423 | 74.6055 | 89.1753 | 53.3280 | 520 | 177 | 519 | 63 | 62 | 98.4127 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3623 | 99.9488 | 96.8254 | 41.7173 | 1952 | 1 | 1952 | 64 | 62 | 96.8750 | |
| jli-custom | SNP | * | map_l100_m1_e0 | het | 99.2812 | 99.1159 | 99.4470 | 63.0672 | 44958 | 401 | 44955 | 250 | 62 | 24.8000 | |
| jli-custom | SNP | * | map_l100_m2_e0 | het | 99.2823 | 99.1336 | 99.4314 | 64.8428 | 45997 | 402 | 45994 | 263 | 62 | 23.5741 | |
| jli-custom | SNP | * | map_l100_m2_e1 | het | 99.2878 | 99.1428 | 99.4333 | 64.8837 | 46496 | 402 | 46493 | 265 | 62 | 23.3962 | |
| ciseli-custom | SNP | ti | map_l150_m1_e0 | het | 73.8384 | 68.2296 | 80.4520 | 83.6682 | 8440 | 3930 | 8437 | 2050 | 62 | 3.0244 | |
| ciseli-custom | SNP | ti | map_l150_m2_e0 | het | 74.3678 | 68.8533 | 80.8425 | 84.6368 | 8869 | 4012 | 8866 | 2101 | 62 | 2.9510 | |
| ciseli-custom | SNP | ti | map_l150_m2_e1 | het | 74.4004 | 68.8974 | 80.8587 | 84.6760 | 8967 | 4048 | 8964 | 2122 | 62 | 2.9218 | |
| ciseli-custom | SNP | tv | map_l125_m2_e0 | het | 74.6164 | 68.4639 | 81.9839 | 81.7497 | 7149 | 3293 | 7149 | 1571 | 62 | 3.9465 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.9169 | 99.3027 | 98.5341 | 69.1612 | 4415 | 31 | 4369 | 65 | 62 | 95.3846 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.6415 | 96.0148 | 97.2764 | 66.3029 | 1301 | 54 | 2643 | 74 | 62 | 83.7838 | |
| cchapple-custom | INDEL | I1_5 | HG002complexvar | het | 99.2036 | 98.7960 | 99.6147 | 56.4110 | 17970 | 219 | 19130 | 74 | 62 | 83.7838 | |
| cchapple-custom | SNP | * | map_l250_m1_e0 | * | 96.0890 | 95.7906 | 96.3892 | 89.6069 | 6918 | 304 | 6914 | 259 | 62 | 23.9382 | |
| ciseli-custom | INDEL | D1_5 | map_l150_m2_e1 | * | 74.1635 | 68.7661 | 80.4805 | 92.8937 | 535 | 243 | 536 | 130 | 62 | 47.6923 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 27.8146 | 34.4262 | 23.3333 | 82.2835 | 21 | 40 | 21 | 69 | 62 | 89.8551 | |
| ckim-gatk | SNP | ti | map_l100_m2_e0 | het | 92.8437 | 88.2960 | 97.8852 | 81.4673 | 27038 | 3584 | 27031 | 584 | 62 | 10.6164 | |
| ckim-gatk | SNP | ti | map_l100_m2_e1 | het | 92.9104 | 88.4076 | 97.8964 | 81.4552 | 27371 | 3589 | 27364 | 588 | 62 | 10.5442 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 94.8557 | 99.0868 | 90.9713 | 82.4616 | 868 | 8 | 665 | 66 | 62 | 93.9394 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3615 | 99.8976 | 96.8719 | 41.6063 | 1951 | 2 | 1951 | 63 | 62 | 98.4127 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3863 | 99.8976 | 96.9200 | 41.4826 | 1951 | 2 | 1951 | 62 | 62 | 100.0000 | |
| astatham-gatk | SNP | * | HG002complexvar | * | 99.1835 | 98.3938 | 99.9860 | 19.2643 | 742264 | 12117 | 742112 | 104 | 62 | 59.6154 | |
| anovak-vg | INDEL | D1_5 | map_l100_m0_e0 | * | 82.9849 | 83.7775 | 82.2072 | 86.7066 | 723 | 140 | 730 | 158 | 62 | 39.2405 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 86.5003 | 83.7811 | 89.4019 | 58.5292 | 842 | 163 | 852 | 101 | 62 | 61.3861 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.2930 | 95.5286 | 99.1239 | 61.6524 | 8033 | 376 | 8033 | 71 | 62 | 87.3239 | |
| bgallagher-sentieon | SNP | * | map_l150_m2_e0 | * | 99.1151 | 99.3470 | 98.8842 | 77.1865 | 31644 | 208 | 31638 | 357 | 62 | 17.3669 | |
| bgallagher-sentieon | SNP | * | map_l150_m2_e1 | * | 99.1218 | 99.3542 | 98.8904 | 77.2353 | 32002 | 208 | 31996 | 359 | 62 | 17.2702 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.5233 | 95.1335 | 95.9163 | 58.0490 | 2815 | 144 | 2842 | 121 | 62 | 51.2397 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.1198 | 98.2713 | 92.1642 | 62.1469 | 739 | 13 | 741 | 63 | 62 | 98.4127 | |
| jli-custom | INDEL | * | HG002complexvar | hetalt | 92.1678 | 86.8343 | 98.1995 | 67.3509 | 3212 | 487 | 3436 | 63 | 62 | 98.4127 | |
| hfeng-pmm1 | INDEL | D16_PLUS | HG002compoundhet | * | 95.0512 | 93.1226 | 97.0614 | 33.7659 | 2180 | 161 | 2180 | 66 | 62 | 93.9394 | |
| jlack-gatk | INDEL | * | HG002complexvar | hetalt | 94.5505 | 91.1868 | 98.1719 | 68.2876 | 3373 | 326 | 3598 | 67 | 62 | 92.5373 | |
| jlack-gatk | INDEL | * | HG002compoundhet | hetalt | 94.2807 | 89.4162 | 99.7049 | 50.9823 | 22515 | 2665 | 22637 | 67 | 62 | 92.5373 | |
| hfeng-pmm2 | INDEL | I1_5 | HG002compoundhet | het | 89.4149 | 87.4118 | 91.5119 | 86.7066 | 743 | 107 | 690 | 64 | 62 | 96.8750 | |
| hfeng-pmm2 | SNP | * | map_siren | * | 99.6789 | 99.6758 | 99.6819 | 56.1450 | 145754 | 474 | 145731 | 465 | 62 | 13.3333 | |
| hfeng-pmm3 | INDEL | D16_PLUS | * | het | 97.3472 | 97.4992 | 97.1956 | 74.5540 | 3080 | 79 | 2842 | 82 | 62 | 75.6098 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 95.5611 | 96.0968 | 95.0314 | 82.9837 | 1748 | 71 | 1511 | 79 | 62 | 78.4810 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 95.5611 | 96.0968 | 95.0314 | 82.9837 | 1748 | 71 | 1511 | 79 | 62 | 78.4810 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.5421 | 99.7007 | 99.3840 | 44.2028 | 10326 | 31 | 10326 | 64 | 61 | 95.3125 | |
| hfeng-pmm1 | INDEL | D16_PLUS | * | het | 97.0973 | 97.6575 | 96.5435 | 74.8637 | 3085 | 74 | 2849 | 102 | 61 | 59.8039 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 95.1724 | 96.1517 | 94.2128 | 83.1481 | 1749 | 70 | 1514 | 93 | 61 | 65.5914 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 95.1724 | 96.1517 | 94.2128 | 83.1481 | 1749 | 70 | 1514 | 93 | 61 | 65.5914 | |