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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
57751-57800 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | * | HG002complexvar | hetalt | 96.4173 | 94.5931 | 98.3131 | 68.7891 | 3499 | 200 | 3730 | 64 | 63 | 98.4375 | |
| jlack-gatk | INDEL | D6_15 | HG002complexvar | homalt | 99.0234 | 99.7434 | 98.3137 | 61.3807 | 1166 | 3 | 1166 | 20 | 19 | 95.0000 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l150_m2_e1 | * | 97.8696 | 97.4293 | 98.3139 | 88.2398 | 758 | 20 | 758 | 13 | 6 | 46.1538 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 91.1346 | 84.9322 | 98.3142 | 43.5277 | 13094 | 2323 | 13472 | 231 | 203 | 87.8788 | |
| gduggal-snapvard | INDEL | D1_5 | map_l125_m0_e0 | homalt | 94.2676 | 90.5405 | 98.3146 | 84.3310 | 134 | 14 | 175 | 3 | 3 | 100.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | map_l150_m2_e1 | * | 98.4039 | 98.4934 | 98.3146 | 90.3068 | 523 | 8 | 525 | 9 | 2 | 22.2222 | |
| ckim-isaac | INDEL | D1_5 | map_l150_m2_e1 | het | 79.5911 | 66.8582 | 98.3146 | 91.5439 | 349 | 173 | 350 | 6 | 2 | 33.3333 | |
| ltrigg-rtg2 | INDEL | * | map_l250_m1_e0 | het | 94.2599 | 90.5263 | 98.3146 | 91.6275 | 172 | 18 | 175 | 3 | 0 | 0.0000 | |
| gduggal-snapfb | INDEL | * | map_l100_m1_e0 | homalt | 96.6439 | 95.0285 | 98.3151 | 86.5465 | 1166 | 61 | 1167 | 20 | 12 | 60.0000 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6636 | 97.0202 | 98.3156 | 79.8607 | 1107 | 34 | 1109 | 19 | 14 | 73.6842 | |
| raldana-dualsentieon | INDEL | D1_5 | map_l150_m2_e1 | * | 97.8058 | 97.3008 | 98.3161 | 87.6421 | 757 | 21 | 759 | 13 | 4 | 30.7692 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 85.0898 | 75.0000 | 98.3165 | 64.4737 | 285 | 95 | 292 | 5 | 5 | 100.0000 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.1222 | 94.0230 | 98.3173 | 61.3742 | 409 | 26 | 409 | 7 | 4 | 57.1429 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.5480 | 98.7793 | 98.3178 | 63.7657 | 1052 | 13 | 1052 | 18 | 14 | 77.7778 | |
| hfeng-pmm2 | INDEL | I1_5 | map_l150_m2_e1 | * | 98.4994 | 98.6817 | 98.3178 | 90.3967 | 524 | 7 | 526 | 9 | 2 | 22.2222 | |
| gduggal-bwafb | INDEL | * | map_l100_m2_e0 | * | 96.2600 | 94.2865 | 98.3179 | 84.2676 | 3482 | 211 | 3507 | 60 | 20 | 33.3333 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 94.1296 | 90.2834 | 98.3180 | 72.2646 | 669 | 72 | 643 | 11 | 9 | 81.8182 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 80.7906 | 68.5669 | 98.3181 | 40.6653 | 2622 | 1202 | 2806 | 48 | 41 | 85.4167 | |
| raldana-dualsentieon | INDEL | I1_5 | map_l100_m1_e0 | het | 97.8051 | 97.2973 | 98.3182 | 81.2333 | 756 | 21 | 760 | 13 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | * | map_l125_m2_e0 | * | 98.3167 | 98.3151 | 98.3182 | 89.0905 | 2159 | 37 | 2163 | 37 | 8 | 21.6216 | |
| mlin-fermikit | SNP | tv | map_l100_m0_e0 | het | 56.5874 | 39.7258 | 98.3185 | 59.7124 | 2869 | 4353 | 2865 | 49 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | * | map_l100_m2_e0 | hetalt | 94.6259 | 91.2000 | 98.3193 | 88.0762 | 114 | 11 | 117 | 2 | 1 | 50.0000 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0614 | 99.8136 | 98.3203 | 43.6922 | 10712 | 20 | 10712 | 183 | 5 | 2.7322 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.5533 | 98.7871 | 98.3205 | 78.4263 | 10670 | 131 | 10713 | 183 | 3 | 1.6393 | |
| rpoplin-dv42 | INDEL | * | map_l150_m2_e1 | * | 97.8375 | 97.3593 | 98.3205 | 99.0326 | 1401 | 38 | 1405 | 24 | 12 | 50.0000 | |
| jpowers-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.0596 | 99.8095 | 98.3209 | 76.9759 | 524 | 1 | 527 | 9 | 6 | 66.6667 | |
| dgrover-gatk | INDEL | D6_15 | * | het | 98.8856 | 99.4565 | 98.3212 | 62.9800 | 11529 | 63 | 11479 | 196 | 167 | 85.2041 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.6411 | 96.9703 | 98.3214 | 47.5930 | 19972 | 624 | 19973 | 341 | 336 | 98.5337 | |
| bgallagher-sentieon | SNP | * | map_l150_m2_e0 | het | 98.7961 | 99.2748 | 98.3220 | 79.7541 | 19987 | 146 | 19981 | 341 | 50 | 14.6628 | |
| gduggal-bwafb | INDEL | D1_5 | map_siren | * | 98.1690 | 98.0164 | 98.3220 | 81.5743 | 3459 | 70 | 3457 | 59 | 15 | 25.4237 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l150_m1_e0 | het | 97.8207 | 97.3244 | 98.3221 | 88.5998 | 291 | 8 | 293 | 5 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | I1_5 | map_l150_m1_e0 | het | 98.1575 | 97.9933 | 98.3221 | 89.8398 | 293 | 6 | 293 | 5 | 1 | 20.0000 | |
| gduggal-bwafb | INDEL | * | map_siren | het | 96.6142 | 94.9645 | 98.3223 | 79.9104 | 4281 | 227 | 4454 | 76 | 20 | 26.3158 | |
| bgallagher-sentieon | SNP | tv | map_l125_m2_e1 | het | 98.8786 | 99.4409 | 98.3226 | 76.2835 | 10494 | 59 | 10492 | 179 | 22 | 12.2905 | |
| jli-custom | INDEL | D1_5 | map_l125_m2_e1 | het | 98.5762 | 98.8312 | 98.3226 | 85.8499 | 761 | 9 | 762 | 13 | 3 | 23.0769 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.3830 | 98.4436 | 98.3226 | 73.6125 | 1518 | 24 | 1524 | 26 | 5 | 19.2308 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 83.6943 | 72.8549 | 98.3229 | 36.6534 | 467 | 174 | 469 | 8 | 6 | 75.0000 | |
| jlack-gatk | INDEL | * | * | het | 98.8624 | 99.4076 | 98.3232 | 61.7242 | 192983 | 1150 | 192623 | 3285 | 1088 | 33.1202 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.3146 | 98.3051 | 98.3240 | 64.3426 | 174 | 3 | 176 | 3 | 1 | 33.3333 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 54.0780 | 37.2951 | 98.3240 | 67.3953 | 182 | 306 | 176 | 3 | 3 | 100.0000 | |
| mlin-fermikit | INDEL | D1_5 | segdup | homalt | 98.3264 | 98.3287 | 98.3240 | 93.5215 | 353 | 6 | 352 | 6 | 6 | 100.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l100_m0_e0 | het | 98.7377 | 99.1540 | 98.3250 | 82.6403 | 586 | 5 | 587 | 10 | 1 | 10.0000 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 89.7782 | 82.5984 | 98.3250 | 32.1288 | 4870 | 1026 | 4931 | 84 | 71 | 84.5238 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 89.7782 | 82.5984 | 98.3250 | 32.1288 | 4870 | 1026 | 4931 | 84 | 71 | 84.5238 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.1723 | 98.0188 | 98.3264 | 71.8409 | 940 | 19 | 940 | 16 | 9 | 56.2500 | |
| dgrover-gatk | INDEL | * | map_l100_m2_e1 | * | 98.3513 | 98.3759 | 98.3267 | 86.6891 | 3695 | 61 | 3702 | 63 | 16 | 25.3968 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 73.4050 | 58.5620 | 98.3268 | 40.8270 | 1067 | 755 | 999 | 17 | 15 | 88.2353 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.6511 | 96.9845 | 98.3269 | 41.1237 | 23800 | 740 | 23802 | 405 | 370 | 91.3580 | |
| raldana-dualsentieon | SNP | * | map_l150_m2_e1 | het | 98.5420 | 98.7576 | 98.3273 | 78.0672 | 20110 | 253 | 20104 | 342 | 4 | 1.1696 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.5168 | 96.7193 | 98.3276 | 70.0415 | 4835 | 164 | 4821 | 82 | 63 | 76.8293 | |