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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
16001-16050 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | SNP | tv | map_l250_m2_e0 | het | 97.7583 | 97.7835 | 97.7331 | 90.3173 | 1897 | 43 | 1897 | 44 | 3 | 6.8182 | |
| gduggal-bwaplat | INDEL | * | map_siren | homalt | 83.1471 | 71.4501 | 99.4235 | 85.0984 | 1897 | 758 | 1897 | 11 | 10 | 90.9091 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.0605 | 98.0859 | 98.0352 | 64.9002 | 1896 | 37 | 1896 | 38 | 35 | 92.1053 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m2_e0 | * | 98.8260 | 98.7990 | 98.8530 | 85.3498 | 1892 | 23 | 1896 | 22 | 5 | 22.7273 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1103 | 98.0341 | 98.1865 | 65.1058 | 1895 | 38 | 1895 | 35 | 35 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.8091 | 97.7471 | 99.8946 | 29.7927 | 1909 | 44 | 1895 | 2 | 2 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | map_l100_m2_e0 | * | 97.0041 | 98.7467 | 95.3219 | 88.2074 | 1891 | 24 | 1895 | 93 | 8 | 8.6022 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.0078 | 97.9824 | 98.0331 | 65.1766 | 1894 | 39 | 1894 | 38 | 36 | 94.7368 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.0078 | 97.9824 | 98.0331 | 65.1766 | 1894 | 39 | 1894 | 38 | 36 | 94.7368 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 82.5452 | 70.6189 | 99.3183 | 55.6924 | 1894 | 788 | 1894 | 13 | 13 | 100.0000 | |
| hfeng-pmm1 | SNP | tv | map_l250_m2_e0 | het | 98.1856 | 97.6289 | 98.7487 | 88.3106 | 1894 | 46 | 1894 | 24 | 3 | 12.5000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.6653 | 98.1228 | 99.2138 | 75.9182 | 1934 | 37 | 1893 | 15 | 7 | 46.6667 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.6653 | 98.1228 | 99.2138 | 75.9182 | 1934 | 37 | 1893 | 15 | 7 | 46.6667 | |
| jli-custom | SNP | tv | map_l250_m2_e1 | het | 97.5522 | 96.3359 | 98.7996 | 86.4727 | 1893 | 72 | 1893 | 23 | 8 | 34.7826 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5626 | 98.0720 | 99.0581 | 75.3578 | 1933 | 38 | 1893 | 18 | 10 | 55.5556 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5626 | 98.0720 | 99.0581 | 75.3578 | 1933 | 38 | 1893 | 18 | 10 | 55.5556 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 83.1319 | 71.6717 | 98.9545 | 46.3244 | 1895 | 749 | 1893 | 20 | 17 | 85.0000 | |
| ltrigg-rtg1 | INDEL | I1_5 | HG002complexvar | hetalt | 97.3210 | 95.3071 | 99.4220 | 76.8604 | 1645 | 81 | 1892 | 11 | 11 | 100.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l100_m2_e0 | * | 98.7206 | 98.6423 | 98.7990 | 83.5904 | 1889 | 26 | 1892 | 23 | 9 | 39.1304 | |
| raldana-dualsentieon | INDEL | I16_PLUS | * | hetalt | 94.2306 | 89.1325 | 99.9472 | 55.4588 | 1870 | 228 | 1892 | 1 | 1 | 100.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.6137 | 98.0720 | 99.1614 | 75.6166 | 1933 | 38 | 1892 | 16 | 8 | 50.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.6137 | 98.0720 | 99.1614 | 75.6166 | 1933 | 38 | 1892 | 16 | 8 | 50.0000 | |
| gduggal-snapvard | INDEL | I6_15 | * | homalt | 43.3535 | 28.2462 | 93.2020 | 23.7129 | 1762 | 4476 | 1892 | 138 | 135 | 97.8261 | |
| gduggal-snapfb | SNP | tv | map_l250_m2_e1 | het | 94.3848 | 96.2341 | 92.6053 | 87.5145 | 1891 | 74 | 1891 | 151 | 50 | 33.1126 | |
| gduggal-bwavard | SNP | tv | map_l250_m2_e0 | het | 85.1643 | 97.8866 | 75.3687 | 92.7134 | 1899 | 41 | 1891 | 618 | 13 | 2.1036 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5365 | 98.0213 | 99.0571 | 76.1911 | 1932 | 39 | 1891 | 18 | 6 | 33.3333 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5365 | 98.0213 | 99.0571 | 76.1911 | 1932 | 39 | 1891 | 18 | 6 | 33.3333 | |
| gduggal-snapvard | SNP | tv | map_l250_m2_e1 | het | 80.5690 | 96.7430 | 69.0285 | 92.1093 | 1901 | 64 | 1890 | 848 | 29 | 3.4198 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 64.6148 | 54.0919 | 80.2207 | 60.1084 | 1236 | 1049 | 1890 | 466 | 171 | 36.6953 | |
| jlack-gatk | SNP | tv | map_l250_m2_e0 | het | 89.1930 | 97.4227 | 82.2454 | 94.1018 | 1890 | 50 | 1890 | 408 | 18 | 4.4118 | |
| jlack-gatk | INDEL | D1_5 | map_l100_m2_e0 | * | 95.2850 | 98.5379 | 92.2401 | 87.2851 | 1887 | 28 | 1890 | 159 | 11 | 6.9182 | |
| eyeh-varpipe | INDEL | I1_5 | map_siren | het | 97.1764 | 97.3825 | 96.9713 | 77.3988 | 1637 | 44 | 1889 | 59 | 41 | 69.4915 | |
| jli-custom | INDEL | D1_5 | map_l100_m2_e0 | * | 98.6673 | 98.5379 | 98.7971 | 83.0195 | 1887 | 28 | 1889 | 23 | 8 | 34.7826 | |
| anovak-vg | INDEL | * | segdup | * | 73.2929 | 72.4961 | 74.1075 | 94.2874 | 1853 | 703 | 1889 | 660 | 536 | 81.2121 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.7996 | 97.7237 | 97.8756 | 64.8324 | 1889 | 44 | 1889 | 41 | 41 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5099 | 97.8184 | 99.2114 | 76.2576 | 1928 | 43 | 1887 | 15 | 6 | 40.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5099 | 97.8184 | 99.2114 | 76.2576 | 1928 | 43 | 1887 | 15 | 6 | 40.0000 | |
| jmaeng-gatk | INDEL | D1_5 | map_l100_m2_e0 | * | 96.9664 | 98.3290 | 95.6412 | 88.3941 | 1883 | 32 | 1887 | 86 | 8 | 9.3023 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l100_m2_e1 | * | 97.6961 | 97.3182 | 98.0769 | 82.8076 | 1887 | 52 | 1887 | 37 | 17 | 45.9459 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5612 | 97.7676 | 99.3678 | 76.3607 | 1927 | 44 | 1886 | 12 | 6 | 50.0000 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5612 | 97.7676 | 99.3678 | 76.3607 | 1927 | 44 | 1886 | 12 | 6 | 50.0000 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 88.5630 | 82.2103 | 95.9796 | 32.1478 | 5661 | 1225 | 1886 | 79 | 51 | 64.5570 | |
| gduggal-snapvard | INDEL | * | map_l125_m2_e1 | het | 83.7912 | 96.0938 | 74.2812 | 90.3789 | 1353 | 55 | 1886 | 653 | 259 | 39.6631 | |
| raldana-dualsentieon | INDEL | I16_PLUS | HG002compoundhet | hetalt | 94.2662 | 89.1543 | 100.0000 | 44.8215 | 1866 | 227 | 1886 | 0 | 0 | ||
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.5673 | 97.5168 | 97.6178 | 66.9009 | 1885 | 48 | 1885 | 46 | 46 | 100.0000 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7091 | 99.9470 | 99.4723 | 72.1242 | 1885 | 1 | 1885 | 10 | 9 | 90.0000 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7091 | 99.9470 | 99.4723 | 72.7691 | 1885 | 1 | 1885 | 10 | 8 | 80.0000 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7617 | 99.8940 | 99.6298 | 72.7247 | 1884 | 2 | 1884 | 7 | 5 | 71.4286 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.5772 | 99.8940 | 99.2624 | 72.0923 | 1884 | 2 | 1884 | 14 | 11 | 78.5714 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.6825 | 99.8940 | 99.4720 | 72.6656 | 1884 | 2 | 1884 | 10 | 8 | 80.0000 | |