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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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74601-74650 / 86044 show all | |||||||||||||||
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.1902 | 91.5599 | 99.1202 | 67.5348 | 10577 | 975 | 10478 | 93 | 44 | 47.3118 | |
| eyeh-varpipe | INDEL | * | map_l125_m2_e0 | * | 96.4662 | 96.0383 | 96.8979 | 94.3332 | 2109 | 87 | 2905 | 93 | 66 | 70.9677 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.8789 | 99.1218 | 96.6667 | 63.6387 | 2709 | 24 | 2697 | 93 | 90 | 96.7742 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.8377 | 98.6970 | 98.9788 | 83.4427 | 9014 | 119 | 9014 | 93 | 10 | 10.7527 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.8377 | 98.6970 | 98.9788 | 83.4427 | 9014 | 119 | 9014 | 93 | 10 | 10.7527 | |
| ckim-isaac | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.5405 | 96.0212 | 99.1085 | 32.5488 | 10305 | 427 | 10339 | 93 | 45 | 48.3871 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 81.5043 | 75.5582 | 88.4663 | 84.8513 | 643 | 208 | 721 | 94 | 7 | 7.4468 | |
| dgrover-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.6673 | 99.8600 | 99.4754 | 57.8446 | 17826 | 25 | 17825 | 94 | 5 | 5.3192 | |
| ckim-vqsr | SNP | tv | map_l150_m2_e0 | * | 65.9681 | 49.6257 | 98.3589 | 92.1554 | 5635 | 5720 | 5634 | 94 | 0 | 0.0000 | |
| ckim-vqsr | SNP | tv | map_l150_m2_e0 | het | 77.8008 | 64.4926 | 98.0294 | 92.2019 | 4677 | 2575 | 4676 | 94 | 0 | 0.0000 | |
| ckim-vqsr | SNP | tv | map_l150_m2_e1 | * | 66.1510 | 49.8261 | 98.3860 | 92.1390 | 5731 | 5771 | 5730 | 94 | 0 | 0.0000 | |
| ckim-vqsr | SNP | tv | map_l150_m2_e1 | het | 77.9198 | 64.6434 | 98.0591 | 92.2018 | 4750 | 2598 | 4749 | 94 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | HG002compoundhet | * | 95.7397 | 95.5147 | 95.9657 | 35.4749 | 2236 | 105 | 2236 | 94 | 91 | 96.8085 | |
| ndellapenna-hhga | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4700 | 99.4059 | 99.5342 | 55.3861 | 20079 | 120 | 20088 | 94 | 83 | 88.2979 | |
| ndellapenna-hhga | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4006 | 99.1437 | 99.6587 | 62.2119 | 27441 | 237 | 27449 | 94 | 60 | 63.8298 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 96.9189 | 96.4670 | 97.3750 | 70.9358 | 3495 | 128 | 3487 | 94 | 86 | 91.4894 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m0_e0 | * | 68.2636 | 57.4739 | 84.0407 | 76.2404 | 496 | 367 | 495 | 94 | 78 | 82.9787 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 75.6798 | 94.7674 | 62.9921 | 72.8632 | 163 | 9 | 160 | 94 | 2 | 2.1277 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 95.5179 | 97.5818 | 93.5395 | 36.9311 | 686 | 17 | 1361 | 94 | 10 | 10.6383 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.1026 | 99.7251 | 98.4878 | 62.3729 | 6167 | 17 | 6122 | 94 | 6 | 6.3830 | |
| jpowers-varprowl | INDEL | * | map_l100_m0_e0 | het | 92.1663 | 93.3399 | 91.0220 | 88.6047 | 953 | 68 | 953 | 94 | 59 | 62.7660 | |
| jpowers-varprowl | INDEL | D1_5 | map_l100_m2_e0 | * | 93.7318 | 92.5326 | 94.9625 | 84.4045 | 1772 | 143 | 1772 | 94 | 63 | 67.0213 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 44.9870 | 55.6604 | 37.7483 | 73.6014 | 59 | 47 | 57 | 94 | 93 | 98.9362 | |
| jpowers-varprowl | SNP | * | map_l100_m2_e1 | homalt | 99.3431 | 99.0286 | 99.6597 | 66.2636 | 27526 | 270 | 27526 | 94 | 69 | 73.4043 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.8845 | 99.1738 | 98.5968 | 78.6472 | 6602 | 55 | 6605 | 94 | 1 | 1.0638 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.5609 | 99.3157 | 97.8175 | 79.7318 | 4209 | 29 | 4213 | 94 | 1 | 1.0638 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 79.8828 | 68.6011 | 95.6054 | 61.8717 | 2045 | 936 | 2045 | 94 | 28 | 29.7872 | |
| gduggal-bwaplat | SNP | * | map_l150_m2_e0 | het | 74.3081 | 59.3950 | 99.2206 | 92.2348 | 11958 | 8175 | 11966 | 94 | 27 | 28.7234 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 91.7798 | 92.5682 | 91.0048 | 77.6662 | 984 | 79 | 951 | 94 | 57 | 60.6383 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 93.0462 | 99.6956 | 87.2283 | 80.4151 | 655 | 2 | 642 | 94 | 57 | 60.6383 | |
| gduggal-bwafb | INDEL | I6_15 | HG002complexvar | het | 87.7628 | 80.4671 | 96.5134 | 49.2661 | 1895 | 460 | 2602 | 94 | 89 | 94.6809 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 74.2459 | 71.4286 | 77.2947 | 60.6089 | 435 | 174 | 320 | 94 | 92 | 97.8723 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 44.0002 | 28.5292 | 96.1301 | 45.3174 | 2029 | 5083 | 2335 | 94 | 92 | 97.8723 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 94.4767 | 93.8476 | 95.1143 | 74.6842 | 2044 | 134 | 1830 | 94 | 84 | 89.3617 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 91.8474 | 91.0470 | 92.6620 | 63.5458 | 1200 | 118 | 1187 | 94 | 90 | 95.7447 | |
| hfeng-pmm3 | SNP | ti | map_l100_m2_e1 | het | 99.5633 | 99.4315 | 99.6955 | 65.7255 | 30784 | 176 | 30777 | 94 | 9 | 9.5745 | |
| gduggal-snapplat | INDEL | D1_5 | map_l125_m2_e0 | het | 85.2845 | 82.4607 | 88.3085 | 93.5494 | 630 | 134 | 710 | 94 | 20 | 21.2766 | |
| ckim-gatk | INDEL | * | segdup | * | 97.7045 | 99.0219 | 96.4218 | 95.7792 | 2531 | 25 | 2533 | 94 | 10 | 10.6383 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.0263 | 96.6909 | 99.3990 | 68.1693 | 15545 | 532 | 15546 | 94 | 71 | 75.5319 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.0263 | 96.6909 | 99.3990 | 68.1693 | 15545 | 532 | 15546 | 94 | 71 | 75.5319 | |
| ciseli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 96.7044 | 99.1299 | 94.3948 | 61.8169 | 1595 | 14 | 1583 | 94 | 27 | 28.7234 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 46.3519 | 40.9091 | 53.4653 | 59.0264 | 99 | 143 | 108 | 94 | 71 | 75.5319 | |
| anovak-vg | SNP | * | map_l125_m1_e0 | homalt | 89.5021 | 81.4552 | 99.3132 | 65.1171 | 13770 | 3135 | 13593 | 94 | 78 | 82.9787 | |
| anovak-vg | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 97.3224 | 97.0558 | 97.5904 | 32.2861 | 3791 | 115 | 3807 | 94 | 61 | 64.8936 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 88.0992 | 92.7022 | 83.9316 | 81.2018 | 470 | 37 | 491 | 94 | 76 | 80.8511 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.0554 | 100.0000 | 96.1851 | 55.9528 | 2370 | 0 | 2370 | 94 | 93 | 98.9362 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 60.9623 | 54.4271 | 69.2810 | 72.5314 | 209 | 175 | 212 | 94 | 51 | 54.2553 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 30.5882 | 23.0769 | 45.3488 | 45.7413 | 39 | 130 | 78 | 94 | 74 | 78.7234 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 63.7080 | 51.7647 | 82.8154 | 52.5585 | 440 | 410 | 453 | 94 | 66 | 70.2128 | |
| asubramanian-gatk | INDEL | D1_5 | * | hetalt | 96.4051 | 93.9092 | 99.0373 | 64.2371 | 9621 | 624 | 9670 | 94 | 88 | 93.6170 | |