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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
60101-60150 / 86044 show all | |||||||||||||||
| ltrigg-rtg2 | SNP | * | map_siren | het | 99.2163 | 98.7812 | 99.6552 | 46.0328 | 89881 | 1109 | 89887 | 311 | 15 | 4.8232 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 36.9719 | 33.9924 | 40.5239 | 46.0310 | 3215 | 6243 | 3218 | 4723 | 4680 | 99.0896 | |
| ckim-isaac | INDEL | D1_5 | * | het | 97.9869 | 97.6340 | 98.3423 | 46.0249 | 85502 | 2072 | 85013 | 1433 | 986 | 68.8067 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 44.7458 | 92.9577 | 29.4643 | 46.0241 | 66 | 5 | 66 | 158 | 142 | 89.8734 | |
| hfeng-pmm3 | INDEL | I16_PLUS | HG002compoundhet | hetalt | 96.1827 | 92.6899 | 99.9490 | 46.0226 | 1940 | 153 | 1960 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 100.0000 | 100.0000 | 100.0000 | 46.0157 | 481 | 0 | 481 | 0 | 0 | ||
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 95.5224 | 100.0000 | 91.4286 | 46.0154 | 192 | 0 | 192 | 18 | 17 | 94.4444 | |
| gduggal-snapfb | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.5691 | 99.7274 | 99.4112 | 46.0147 | 2195 | 6 | 2195 | 13 | 6 | 46.1538 | |
| dgrover-gatk | INDEL | I16_PLUS | HG002compoundhet | hetalt | 96.3626 | 93.0244 | 99.9492 | 46.0126 | 1947 | 146 | 1969 | 1 | 1 | 100.0000 | |
| jlack-gatk | SNP | ti | tech_badpromoters | * | 98.2659 | 100.0000 | 96.5909 | 46.0123 | 85 | 0 | 85 | 3 | 0 | 0.0000 | |
| anovak-vg | INDEL | I16_PLUS | * | het | 20.3076 | 12.3988 | 56.0773 | 46.0104 | 337 | 2381 | 406 | 318 | 57 | 17.9245 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.9303 | 100.0000 | 99.8608 | 46.0035 | 2152 | 0 | 2152 | 3 | 3 | 100.0000 | |
| raldana-dualsentieon | SNP | * | tech_badpromoters | homalt | 98.1366 | 98.7500 | 97.5309 | 46.0000 | 79 | 1 | 79 | 2 | 2 | 100.0000 | |
| gduggal-bwafb | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.7673 | 99.3559 | 98.1857 | 45.9987 | 7404 | 48 | 7414 | 137 | 23 | 16.7883 | |
| ckim-isaac | INDEL | D1_5 | * | hetalt | 92.0397 | 86.6959 | 98.0855 | 45.9935 | 8882 | 1363 | 9222 | 180 | 168 | 93.3333 | |
| hfeng-pmm3 | SNP | * | tech_badpromoters | * | 99.3590 | 98.7261 | 100.0000 | 45.9930 | 155 | 2 | 155 | 0 | 0 | ||
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 63.1989 | 46.4849 | 98.6799 | 45.9893 | 324 | 373 | 299 | 4 | 4 | 100.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | HG002compoundhet | hetalt | 96.2598 | 92.8333 | 99.9491 | 45.9846 | 1943 | 150 | 1963 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 97.5125 | 95.6457 | 99.4536 | 45.9819 | 13421 | 611 | 13651 | 75 | 74 | 98.6667 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.8249 | 99.6503 | 100.0000 | 45.9813 | 855 | 3 | 867 | 0 | 0 | ||
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.1247 | 99.5589 | 96.7314 | 45.9773 | 9479 | 42 | 9470 | 320 | 309 | 96.5625 | |
| gduggal-bwafb | SNP | * | HG002compoundhet | * | 97.9194 | 99.0744 | 96.7911 | 45.9764 | 25583 | 239 | 25699 | 852 | 222 | 26.0563 | |
| gduggal-bwaplat | INDEL | D6_15 | HG002compoundhet | * | 81.3435 | 69.7154 | 97.6272 | 45.9650 | 6296 | 2735 | 6295 | 153 | 109 | 71.2418 | |
| raldana-dualsentieon | INDEL | * | func_cds | het | 98.5959 | 98.1308 | 99.0654 | 45.9596 | 210 | 4 | 212 | 2 | 0 | 0.0000 | |
| eyeh-varpipe | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.1915 | 99.5930 | 94.9031 | 45.9580 | 18109 | 74 | 17428 | 936 | 71 | 7.5855 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 96.2199 | 92.7152 | 100.0000 | 45.9559 | 140 | 11 | 147 | 0 | 0 | ||
| raldana-dualsentieon | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.9303 | 100.0000 | 99.8608 | 45.9493 | 2152 | 0 | 2152 | 3 | 3 | 100.0000 | |
| anovak-vg | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.3610 | 98.4844 | 98.2380 | 45.9412 | 6173 | 95 | 6300 | 113 | 46 | 40.7080 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.6717 | 99.6061 | 99.7373 | 45.9408 | 2276 | 9 | 2278 | 6 | 3 | 50.0000 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.1590 | 96.0055 | 98.3406 | 45.9292 | 36388 | 1514 | 49009 | 827 | 740 | 89.4800 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 77.6152 | 64.0108 | 98.5632 | 45.9265 | 10693 | 6012 | 10153 | 148 | 131 | 88.5135 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 77.6152 | 64.0108 | 98.5632 | 45.9265 | 10693 | 6012 | 10153 | 148 | 131 | 88.5135 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 58.4346 | 41.3660 | 99.4845 | 45.9233 | 2350 | 3331 | 2316 | 12 | 11 | 91.6667 | |
| dgrover-gatk | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.9262 | 99.9016 | 99.9508 | 45.9204 | 4061 | 4 | 4061 | 2 | 1 | 50.0000 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.2868 | 95.8815 | 98.7340 | 45.9174 | 14015 | 602 | 39539 | 507 | 431 | 85.0099 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 97.9533 | 99.6209 | 96.3407 | 45.9172 | 3153 | 12 | 3133 | 119 | 118 | 99.1597 | |
| ckim-dragen | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.8109 | 99.7103 | 95.9825 | 45.9159 | 10327 | 30 | 10321 | 432 | 429 | 99.3056 | |
| astatham-gatk | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.4684 | 98.9668 | 99.9751 | 45.9140 | 4023 | 42 | 4023 | 1 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | func_cds | het | 100.0000 | 100.0000 | 100.0000 | 45.9119 | 85 | 0 | 86 | 0 | 0 | ||
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 73.1236 | 61.8658 | 89.3899 | 45.9110 | 378 | 233 | 337 | 40 | 35 | 87.5000 | |
| astatham-gatk | INDEL | I16_PLUS | HG002compoundhet | hetalt | 96.1827 | 92.6899 | 99.9491 | 45.9080 | 1940 | 153 | 1962 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 73.4367 | 65.0167 | 84.3621 | 45.9065 | 1366 | 735 | 1845 | 342 | 338 | 98.8304 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.0234 | 99.8552 | 98.2053 | 45.9033 | 10342 | 15 | 10342 | 189 | 184 | 97.3545 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.0282 | 99.8648 | 98.2055 | 45.9010 | 10343 | 14 | 10343 | 189 | 184 | 97.3545 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 83.9649 | 79.7856 | 88.6063 | 45.8996 | 25525 | 6467 | 29373 | 3777 | 2366 | 62.6423 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 83.9960 | 76.5257 | 93.0825 | 45.8976 | 7110 | 2181 | 2449 | 182 | 112 | 61.5385 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 83.9960 | 76.5257 | 93.0825 | 45.8976 | 7110 | 2181 | 2449 | 182 | 112 | 61.5385 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.0806 | 99.8938 | 98.2806 | 45.8961 | 10346 | 11 | 10346 | 181 | 177 | 97.7901 | |
| eyeh-varpipe | INDEL | I1_5 | HG002complexvar | homalt | 96.6684 | 96.6984 | 96.6384 | 45.8931 | 13004 | 444 | 12649 | 440 | 434 | 98.6364 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.6399 | 99.2823 | 100.0000 | 45.8931 | 415 | 3 | 415 | 0 | 0 | ||