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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
78051-78100 / 86044 show all | |||||||||||||||
| gduggal-bwavard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 91.6710 | 91.9194 | 91.4238 | 85.3408 | 8395 | 738 | 8283 | 777 | 129 | 16.6023 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.9561 | 99.6411 | 98.2804 | 53.4169 | 8330 | 30 | 8287 | 145 | 135 | 93.1034 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.9561 | 99.6411 | 98.2804 | 53.4169 | 8330 | 30 | 8287 | 145 | 135 | 93.1034 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.1121 | 98.7732 | 95.5059 | 60.7561 | 8293 | 103 | 8288 | 390 | 362 | 92.8205 | |
| raldana-dualsentieon | INDEL | D6_15 | HG002compoundhet | * | 93.9555 | 91.8392 | 96.1717 | 34.6920 | 8294 | 737 | 8290 | 330 | 328 | 99.3939 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.8983 | 99.1544 | 98.6435 | 64.3687 | 8325 | 71 | 8290 | 114 | 105 | 92.1053 | |
| mlin-fermikit | INDEL | I1_5 | HG002compoundhet | * | 72.7922 | 67.2062 | 79.3909 | 62.5413 | 8304 | 4052 | 8290 | 2152 | 2132 | 99.0706 | |
| mlin-fermikit | SNP | tv | segdup | * | 97.8523 | 97.1988 | 98.5147 | 87.3016 | 8293 | 239 | 8291 | 125 | 50 | 40.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.7864 | 99.1544 | 98.4212 | 63.6442 | 8325 | 71 | 8291 | 133 | 121 | 90.9774 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.3938 | 98.9601 | 99.8314 | 43.2370 | 8279 | 87 | 8291 | 14 | 13 | 92.8571 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 64.7210 | 53.4249 | 82.0746 | 70.9149 | 8322 | 7255 | 8292 | 1811 | 1705 | 94.1469 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.8574 | 99.1901 | 98.5270 | 64.5573 | 8328 | 68 | 8294 | 124 | 111 | 89.5161 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.8871 | 99.2258 | 98.5507 | 63.9239 | 8331 | 65 | 8296 | 122 | 109 | 89.3443 | |
| mlin-fermikit | SNP | tv | map_l125_m2_e1 | * | 62.9750 | 49.8289 | 85.5434 | 62.7659 | 8300 | 8357 | 8296 | 1402 | 1229 | 87.6605 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.9346 | 99.2616 | 98.6098 | 64.3360 | 8334 | 62 | 8299 | 117 | 105 | 89.7436 | |
| jli-custom | INDEL | I6_15 | HG002compoundhet | * | 95.9804 | 94.5419 | 97.4633 | 35.3700 | 8297 | 479 | 8299 | 216 | 208 | 96.2963 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 91.1545 | 88.4965 | 93.9771 | 38.2912 | 8370 | 1088 | 8301 | 532 | 447 | 84.0226 | |
| anovak-vg | SNP | tv | segdup | * | 97.7325 | 97.6676 | 97.7974 | 93.3295 | 8333 | 199 | 8303 | 187 | 80 | 42.7807 | |
| ckim-vqsr | SNP | ti | map_l100_m2_e1 | homalt | 61.9730 | 44.9065 | 99.9639 | 77.0833 | 8305 | 10189 | 8305 | 3 | 3 | 100.0000 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 94.0520 | 90.0033 | 98.4822 | 69.9861 | 8220 | 913 | 8305 | 128 | 13 | 10.1562 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 94.0520 | 90.0033 | 98.4822 | 69.9861 | 8220 | 913 | 8305 | 128 | 13 | 10.1562 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.5354 | 97.7762 | 99.3066 | 59.4807 | 8222 | 187 | 8306 | 58 | 19 | 32.7586 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.5930 | 99.2105 | 97.9830 | 63.7025 | 8294 | 66 | 8307 | 171 | 160 | 93.5673 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.5930 | 99.2105 | 97.9830 | 63.7025 | 8294 | 66 | 8307 | 171 | 160 | 93.5673 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.2948 | 99.3780 | 99.2118 | 59.1033 | 8308 | 52 | 8308 | 66 | 66 | 100.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.2948 | 99.3780 | 99.2118 | 59.1033 | 8308 | 52 | 8308 | 66 | 66 | 100.0000 | |
| mlin-fermikit | SNP | tv | map_l100_m1_e0 | het | 69.7650 | 53.9859 | 98.5774 | 56.8653 | 8323 | 7094 | 8315 | 120 | 2 | 1.6667 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 61.8858 | 52.4538 | 75.4536 | 73.3552 | 8433 | 7644 | 8318 | 2706 | 2382 | 88.0266 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 61.8858 | 52.4538 | 75.4536 | 73.3552 | 8433 | 7644 | 8318 | 2706 | 2382 | 88.0266 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.2063 | 99.6651 | 96.7896 | 65.1548 | 8332 | 28 | 8321 | 276 | 275 | 99.6377 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.2063 | 99.6651 | 96.7896 | 65.1548 | 8332 | 28 | 8321 | 276 | 275 | 99.6377 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 65.1709 | 54.2531 | 81.5900 | 69.4864 | 8451 | 7126 | 8323 | 1878 | 1704 | 90.7348 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.4861 | 99.5813 | 99.3911 | 58.2577 | 8325 | 35 | 8325 | 51 | 50 | 98.0392 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.4861 | 99.5813 | 99.3911 | 58.2577 | 8325 | 35 | 8325 | 51 | 50 | 98.0392 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.4624 | 99.5933 | 99.3319 | 58.5091 | 8326 | 34 | 8326 | 56 | 56 | 100.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.4624 | 99.5933 | 99.3319 | 58.5091 | 8326 | 34 | 8326 | 56 | 56 | 100.0000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.2550 | 99.5338 | 98.9778 | 48.7637 | 8327 | 39 | 8327 | 86 | 84 | 97.6744 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.2945 | 99.6172 | 97.0064 | 59.6494 | 8328 | 32 | 8328 | 257 | 256 | 99.6109 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.2945 | 99.6172 | 97.0064 | 59.6494 | 8328 | 32 | 8328 | 257 | 256 | 99.6109 | |
| qzeng-custom | SNP | tv | map_l100_m0_e0 | * | 84.6327 | 75.3158 | 96.5801 | 84.0828 | 8348 | 2736 | 8331 | 295 | 249 | 84.4068 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 97.7765 | 99.6055 | 96.0134 | 48.3178 | 8333 | 33 | 8333 | 346 | 344 | 99.4220 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.4096 | 99.6175 | 99.2025 | 47.1436 | 8334 | 32 | 8334 | 67 | 66 | 98.5075 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.4573 | 99.6653 | 99.2501 | 46.8795 | 8338 | 28 | 8338 | 63 | 60 | 95.2381 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.7335 | 99.7729 | 97.7156 | 45.5716 | 8347 | 19 | 8341 | 195 | 193 | 98.9744 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.0327 | 99.8086 | 98.2688 | 63.7648 | 8344 | 16 | 8344 | 147 | 145 | 98.6395 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.0327 | 99.8086 | 98.2688 | 63.7648 | 8344 | 16 | 8344 | 147 | 145 | 98.6395 | |
| mlin-fermikit | SNP | ti | map_l150_m1_e0 | * | 56.8574 | 42.3346 | 86.5470 | 60.8408 | 8345 | 11367 | 8344 | 1297 | 1150 | 88.6662 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.9740 | 99.8086 | 98.1532 | 63.5791 | 8344 | 16 | 8344 | 157 | 156 | 99.3631 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.9740 | 99.8086 | 98.1532 | 63.5791 | 8344 | 16 | 8344 | 157 | 156 | 99.3631 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.0563 | 99.8206 | 98.3037 | 63.5993 | 8345 | 15 | 8345 | 144 | 142 | 98.6111 | |