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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
9951-10000 / 86044 show all | |||||||||||||||
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 85.8405 | 84.9119 | 86.7896 | 57.5804 | 1784 | 317 | 1695 | 258 | 252 | 97.6744 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 48.6351 | 57.2200 | 42.2902 | 47.0270 | 424 | 317 | 746 | 1018 | 780 | 76.6208 | |
| ciseli-custom | INDEL | D1_5 | map_l125_m2_e0 | * | 76.8250 | 72.2660 | 81.9980 | 90.9083 | 826 | 317 | 829 | 182 | 82 | 45.0549 | |
| ciseli-custom | INDEL | I1_5 | map_l100_m2_e0 | homalt | 54.2174 | 40.3013 | 82.8125 | 83.8994 | 214 | 317 | 212 | 44 | 35 | 79.5455 | |
| ciseli-custom | INDEL | * | map_l150_m1_e0 | het | 66.7585 | 62.9240 | 71.0907 | 93.2928 | 538 | 317 | 541 | 220 | 129 | 58.6364 | |
| ckim-gatk | INDEL | I1_5 | HG002complexvar | * | 99.4404 | 99.0498 | 99.8341 | 56.8511 | 33046 | 317 | 33092 | 55 | 41 | 74.5455 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 85.8873 | 84.9119 | 86.8852 | 57.3613 | 1784 | 317 | 1696 | 256 | 250 | 97.6562 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.4644 | 86.6019 | 99.1783 | 36.1223 | 2049 | 317 | 2052 | 17 | 17 | 100.0000 | |
| ghariani-varprowl | SNP | ti | map_l150_m1_e0 | * | 97.8236 | 98.3918 | 97.2619 | 78.7439 | 19395 | 317 | 19395 | 546 | 133 | 24.3590 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 50.5691 | 51.7504 | 49.4405 | 81.2333 | 340 | 317 | 486 | 497 | 6 | 1.2072 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 34.5477 | 35.3061 | 33.8212 | 42.2578 | 173 | 317 | 647 | 1266 | 1039 | 82.0695 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 3.3537 | 0.0000 | 0.0000 | 11 | 317 | 0 | 0 | 0 | ||
| raldana-dualsentieon | SNP | ti | map_l100_m2_e0 | * | 99.3403 | 99.3525 | 99.3281 | 64.7470 | 48644 | 317 | 48637 | 329 | 19 | 5.7751 | |
| raldana-dualsentieon | SNP | ti | map_l100_m2_e1 | * | 99.3433 | 99.3594 | 99.3272 | 64.7652 | 49168 | 317 | 49161 | 333 | 19 | 5.7057 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.3823 | 95.3945 | 99.4547 | 79.4362 | 6566 | 317 | 6566 | 36 | 9 | 25.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 92.2495 | 86.6245 | 98.6558 | 36.0651 | 2053 | 317 | 2055 | 28 | 21 | 75.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 90.4376 | 83.7686 | 98.2603 | 35.1614 | 1636 | 317 | 1638 | 29 | 15 | 51.7241 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 85.9526 | 84.9119 | 87.0190 | 57.3989 | 1784 | 317 | 1696 | 253 | 247 | 97.6285 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.7354 | 96.2302 | 99.2883 | 62.1142 | 8092 | 317 | 8092 | 58 | 49 | 84.4828 | |
| egarrison-hhga | SNP | * | map_l100_m0_e0 | het | 99.1151 | 98.5051 | 99.7326 | 69.3594 | 20888 | 317 | 20889 | 56 | 24 | 42.8571 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 83.8622 | 76.0787 | 93.4198 | 53.8889 | 1005 | 316 | 1008 | 71 | 48 | 67.6056 | |
| ciseli-custom | INDEL | D1_5 | map_l100_m2_e0 | het | 79.5047 | 74.8408 | 84.7885 | 89.8548 | 940 | 316 | 942 | 169 | 39 | 23.0769 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.3919 | 95.3611 | 99.5111 | 32.7822 | 6496 | 316 | 6513 | 32 | 32 | 100.0000 | |
| hfeng-pmm2 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.0510 | 98.2298 | 99.8861 | 53.8211 | 17535 | 316 | 17534 | 20 | 1 | 5.0000 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 37.7753 | 27.5229 | 60.2000 | 50.3476 | 120 | 316 | 301 | 199 | 199 | 100.0000 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 31.4024 | 23.6715 | 46.6321 | 77.0784 | 98 | 316 | 90 | 103 | 93 | 90.2913 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 63.7102 | 48.2815 | 93.6306 | 83.3598 | 295 | 316 | 294 | 20 | 10 | 50.0000 | |
| gduggal-bwaplat | INDEL | D1_5 | map_l100_m1_e0 | het | 84.4444 | 73.8627 | 98.5651 | 92.5841 | 893 | 316 | 893 | 13 | 4 | 30.7692 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 96.0365 | 96.2201 | 95.8537 | 59.0186 | 8044 | 316 | 8045 | 348 | 182 | 52.2989 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 96.0365 | 96.2201 | 95.8537 | 59.0186 | 8044 | 316 | 8045 | 348 | 182 | 52.2989 | |
| anovak-vg | INDEL | I16_PLUS | HG002complexvar | hetalt | 0.0000 | 5.6716 | 0.0000 | 0.0000 | 19 | 316 | 0 | 0 | 0 | ||
| anovak-vg | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.1744 | 93.3669 | 91.0119 | 70.2375 | 4448 | 316 | 4506 | 445 | 188 | 42.2472 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 89.7688 | 92.5437 | 87.1556 | 81.5735 | 3922 | 316 | 4207 | 620 | 247 | 39.8387 | |
| bgallagher-sentieon | SNP | * | map_l100_m1_e0 | * | 99.4317 | 99.5636 | 99.3001 | 65.4224 | 72087 | 316 | 72076 | 508 | 81 | 15.9449 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 0.0000 | 74.7604 | 0.0000 | 0.0000 | 936 | 316 | 0 | 0 | 0 | ||
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.6420 | 98.4090 | 98.8761 | 66.2789 | 19546 | 316 | 20235 | 230 | 48 | 20.8696 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 50.2642 | 88.4376 | 35.1094 | 44.6429 | 2417 | 316 | 2438 | 4506 | 4477 | 99.3564 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 22.8155 | 12.9477 | 95.9184 | 63.1579 | 47 | 316 | 47 | 2 | 2 | 100.0000 | |
| ghariani-varprowl | SNP | ti | * | homalt | 99.8530 | 99.9608 | 99.7455 | 17.9110 | 802720 | 315 | 802769 | 2048 | 1014 | 49.5117 | |
| hfeng-pmm1 | SNP | * | map_l125_m2_e1 | het | 99.2688 | 98.9372 | 99.6025 | 71.5784 | 29325 | 315 | 29319 | 117 | 29 | 24.7863 | |
| hfeng-pmm1 | SNP | ti | map_l100_m2_e0 | * | 99.5722 | 99.3566 | 99.7887 | 64.0145 | 48646 | 315 | 48639 | 103 | 32 | 31.0680 | |
| hfeng-pmm1 | SNP | ti | map_l100_m2_e1 | * | 99.5757 | 99.3634 | 99.7889 | 64.0077 | 49170 | 315 | 49163 | 104 | 32 | 30.7692 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 73.5605 | 66.5605 | 82.2059 | 36.1952 | 627 | 315 | 2236 | 484 | 477 | 98.5537 | |
| gduggal-bwafb | INDEL | D1_5 | * | homalt | 98.9426 | 99.3562 | 98.5324 | 61.7935 | 48611 | 315 | 48609 | 724 | 697 | 96.2707 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 68.8414 | 56.2500 | 88.6957 | 94.3586 | 405 | 315 | 408 | 52 | 9 | 17.3077 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 0.0000 | 0.3165 | 0.0000 | 0.0000 | 1 | 315 | 0 | 0 | 0 | ||
| ltrigg-rtg1 | SNP | * | map_l250_m1_e0 | het | 96.4484 | 93.3754 | 99.7305 | 78.8925 | 4440 | 315 | 4440 | 12 | 4 | 33.3333 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.6332 | 95.3758 | 100.0000 | 31.9545 | 6497 | 315 | 6514 | 0 | 0 | ||
| rpoplin-dv42 | INDEL | I1_5 | HG002complexvar | * | 99.3509 | 99.0558 | 99.6477 | 56.5141 | 33048 | 315 | 33091 | 117 | 105 | 89.7436 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 84.6939 | 74.8403 | 97.5355 | 31.8035 | 937 | 315 | 1029 | 26 | 23 | 88.4615 | |