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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
71401-71450 / 86044 show all | |||||||||||||||
| mlin-fermikit | INDEL | D1_5 | map_l150_m0_e0 | homalt | 65.0307 | 62.3529 | 67.9487 | 83.1533 | 53 | 32 | 53 | 25 | 21 | 84.0000 | |
| ndellapenna-hhga | INDEL | D1_5 | * | hetalt | 77.7578 | 64.1093 | 98.7893 | 70.8854 | 6568 | 3677 | 6120 | 75 | 63 | 84.0000 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.2126 | 99.1168 | 99.3086 | 83.9167 | 3591 | 32 | 3591 | 25 | 21 | 84.0000 | |
| gduggal-snapvard | INDEL | C6_15 | HG002complexvar | homalt | 0.0000 | 0.0000 | 72.2222 | 75.4768 | 0 | 0 | 65 | 25 | 21 | 84.0000 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 79.8362 | 74.7126 | 85.7143 | 54.9550 | 845 | 286 | 600 | 100 | 84 | 84.0000 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.6972 | 90.3194 | 97.3376 | 61.4215 | 905 | 97 | 914 | 25 | 21 | 84.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.2099 | 97.0828 | 99.3634 | 67.3172 | 15608 | 469 | 15609 | 100 | 84 | 84.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.2099 | 97.0828 | 99.3634 | 67.3172 | 15608 | 469 | 15609 | 100 | 84 | 84.0000 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.8376 | 96.7213 | 94.9698 | 72.2501 | 472 | 16 | 472 | 25 | 21 | 84.0000 | |
| eyeh-varpipe | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 0.0000 | 0.0000 | 73.1183 | 95.8464 | 0 | 0 | 68 | 25 | 21 | 84.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 91.1545 | 88.4965 | 93.9771 | 38.2912 | 8370 | 1088 | 8301 | 532 | 447 | 84.0226 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.9964 | 98.5399 | 99.4571 | 53.2701 | 19572 | 290 | 21802 | 119 | 100 | 84.0336 | |
| qzeng-custom | SNP | * | map_l150_m1_e0 | het | 81.0937 | 70.5218 | 95.3942 | 89.4771 | 13622 | 5694 | 13504 | 652 | 548 | 84.0491 | |
| astatham-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.4126 | 96.9059 | 93.9646 | 79.4691 | 3915 | 125 | 3612 | 232 | 195 | 84.0517 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 6.1644 | 3.6217 | 20.6897 | 83.3652 | 18 | 479 | 18 | 69 | 58 | 84.0580 | |
| asubramanian-gatk | INDEL | I16_PLUS | * | * | 95.8942 | 93.7431 | 98.1463 | 72.1669 | 5978 | 399 | 5983 | 113 | 95 | 84.0708 | |
| qzeng-custom | SNP | ti | map_l250_m2_e0 | * | 74.3996 | 62.1406 | 92.6844 | 95.5558 | 3112 | 1896 | 3104 | 245 | 206 | 84.0816 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 74.1810 | 59.3050 | 99.0185 | 33.0396 | 4847 | 3326 | 4439 | 44 | 37 | 84.0909 | |
| ciseli-custom | INDEL | I1_5 | map_l150_m2_e0 | * | 55.9084 | 48.7476 | 65.5352 | 92.4128 | 253 | 266 | 251 | 132 | 111 | 84.0909 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.6974 | 94.6626 | 98.8216 | 55.5793 | 3689 | 208 | 3690 | 44 | 37 | 84.0909 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 89.1293 | 81.6555 | 98.1092 | 39.4326 | 2190 | 492 | 2283 | 44 | 37 | 84.0909 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 67.8262 | 71.8519 | 64.2276 | 75.9766 | 97 | 38 | 79 | 44 | 37 | 84.0909 | |
| jlack-gatk | INDEL | D6_15 | * | hetalt | 94.6900 | 90.3964 | 99.4119 | 33.6937 | 7389 | 785 | 7438 | 44 | 37 | 84.0909 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 85.6169 | 76.2817 | 97.5556 | 48.0669 | 1473 | 458 | 1756 | 44 | 37 | 84.0909 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 85.6169 | 76.2817 | 97.5556 | 48.0669 | 1473 | 458 | 1756 | 44 | 37 | 84.0909 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.6703 | 94.6112 | 98.8210 | 55.5926 | 3687 | 210 | 3688 | 44 | 37 | 84.0909 | |
| qzeng-custom | SNP | ti | map_l150_m2_e0 | het | 80.5235 | 69.5753 | 95.5605 | 89.8900 | 8962 | 3919 | 8933 | 415 | 349 | 84.0964 | |
| qzeng-custom | SNP | ti | map_l150_m2_e1 | het | 80.5961 | 69.6581 | 95.6089 | 89.9144 | 9066 | 3949 | 9036 | 415 | 349 | 84.0964 | |
| qzeng-custom | SNP | tv | map_l150_m2_e0 | * | 82.9982 | 72.7081 | 96.6811 | 87.1519 | 8256 | 3099 | 8244 | 283 | 238 | 84.0989 | |
| anovak-vg | INDEL | I6_15 | HG002complexvar | * | 48.0486 | 41.4858 | 57.0779 | 45.2877 | 1988 | 2804 | 2008 | 1510 | 1270 | 84.1060 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.5538 | 96.1694 | 98.9788 | 57.8031 | 41675 | 1660 | 41482 | 428 | 360 | 84.1121 | |
| gduggal-bwafb | INDEL | D6_15 | HG002complexvar | * | 93.2387 | 90.0604 | 96.6496 | 53.7803 | 4775 | 527 | 4904 | 170 | 143 | 84.1176 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 32.2728 | 22.6804 | 55.9262 | 35.3818 | 792 | 2700 | 1576 | 1242 | 1045 | 84.1385 | |
| anovak-vg | SNP | * | HG002complexvar | homalt | 98.2895 | 97.5091 | 99.0824 | 19.5966 | 281387 | 7188 | 273293 | 2531 | 2130 | 84.1565 | |
| eyeh-varpipe | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 20.1854 | 11.4278 | 86.3881 | 77.1411 | 437 | 3387 | 641 | 101 | 85 | 84.1584 | |
| anovak-vg | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 47.4248 | 37.3206 | 65.0316 | 30.6257 | 156 | 262 | 411 | 221 | 186 | 84.1629 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 53.5363 | 39.1660 | 84.5632 | 59.4976 | 1869 | 2903 | 1868 | 341 | 287 | 84.1642 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 77.6220 | 87.0095 | 70.0629 | 67.3332 | 1641 | 245 | 1671 | 714 | 601 | 84.1737 | |
| egarrison-hhga | INDEL | * | * | * | 97.4253 | 97.1646 | 97.6874 | 75.7607 | 334773 | 9769 | 335276 | 7937 | 6682 | 84.1880 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 50.1080 | 34.9234 | 88.6547 | 58.7648 | 1984 | 3697 | 1977 | 253 | 213 | 84.1897 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3072 | 99.1321 | 99.4829 | 51.2667 | 3655 | 32 | 3655 | 19 | 16 | 84.2105 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.0553 | 90.6080 | 97.7752 | 66.9888 | 1669 | 173 | 1670 | 38 | 32 | 84.2105 | |
| qzeng-custom | SNP | ti | map_l125_m0_e0 | * | 76.6106 | 63.8536 | 95.7374 | 88.8132 | 8149 | 4613 | 8108 | 361 | 304 | 84.2105 | |
| qzeng-custom | SNP | ti | map_l250_m2_e1 | * | 74.5851 | 62.3719 | 92.7460 | 95.5643 | 3166 | 1910 | 3158 | 247 | 208 | 84.2105 | |
| ckim-dragen | SNP | * | map_l150_m0_e0 | homalt | 99.3015 | 99.0707 | 99.5334 | 70.2317 | 4051 | 38 | 4053 | 19 | 16 | 84.2105 | |
| ckim-dragen | SNP | * | map_l250_m2_e0 | homalt | 99.1424 | 98.9948 | 99.2905 | 83.9458 | 2659 | 27 | 2659 | 19 | 16 | 84.2105 | |
| ckim-dragen | SNP | * | map_l250_m2_e1 | homalt | 99.1340 | 98.9698 | 99.2986 | 84.0205 | 2690 | 28 | 2690 | 19 | 16 | 84.2105 | |
| ckim-vqsr | SNP | tv | * | homalt | 98.8369 | 97.7055 | 99.9948 | 20.5893 | 368470 | 8653 | 368456 | 19 | 16 | 84.2105 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.9509 | 94.7199 | 99.2895 | 61.7800 | 7965 | 444 | 7965 | 57 | 48 | 84.2105 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | HG002complexvar | * | 92.2852 | 87.0130 | 98.2375 | 52.4691 | 1139 | 170 | 1059 | 19 | 16 | 84.2105 | |