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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
79301-79350 / 86044 show all | |||||||||||||||
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 12.6208 | 7.7147 | 34.6667 | 87.4161 | 53 | 634 | 52 | 98 | 77 | 78.5714 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 92.5569 | 94.9365 | 90.2936 | 47.5778 | 11887 | 634 | 11256 | 1210 | 1034 | 85.4545 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.8922 | 94.2909 | 99.6412 | 27.0291 | 10471 | 634 | 10553 | 38 | 38 | 100.0000 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.6327 | 96.9169 | 98.3591 | 48.8223 | 19961 | 635 | 19961 | 333 | 328 | 98.4985 | |
| ciseli-custom | SNP | ti | map_l125_m0_e0 | homalt | 86.4046 | 85.8606 | 86.9555 | 67.4980 | 3856 | 635 | 3853 | 578 | 472 | 81.6609 | |
| gduggal-bwavard | SNP | tv | map_siren | het | 95.7305 | 97.7804 | 93.7647 | 72.5806 | 27974 | 635 | 27865 | 1853 | 145 | 7.8252 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 12.5633 | 8.8953 | 21.3793 | 49.9136 | 62 | 635 | 62 | 228 | 224 | 98.2456 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.8827 | 94.2729 | 99.6411 | 27.0328 | 10469 | 636 | 10551 | 38 | 38 | 100.0000 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 7.2121 | 4.3609 | 20.8333 | 84.0266 | 29 | 636 | 40 | 152 | 95 | 62.5000 | |
| qzeng-custom | INDEL | * | map_siren | het | 88.2436 | 85.8917 | 90.7279 | 86.0479 | 3872 | 636 | 4325 | 442 | 93 | 21.0407 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 0.7800 | 0.0000 | 0.0000 | 5 | 636 | 0 | 0 | 0 | ||
| jpowers-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 0.7800 | 0.0000 | 0.0000 | 5 | 636 | 0 | 0 | 0 | ||
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.9301 | 95.6489 | 98.2460 | 63.4208 | 13981 | 636 | 13611 | 243 | 222 | 91.3580 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.4489 | 97.9134 | 98.9903 | 69.4877 | 29844 | 636 | 29412 | 300 | 222 | 74.0000 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.4489 | 97.9134 | 98.9903 | 69.4877 | 29844 | 636 | 29412 | 300 | 222 | 74.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5102 | 97.4083 | 99.6374 | 38.9351 | 23904 | 636 | 23906 | 87 | 70 | 80.4598 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 94.8171 | 94.6358 | 94.9992 | 46.8433 | 11238 | 637 | 11246 | 592 | 535 | 90.3716 | |
| gduggal-bwafb | SNP | * | map_l100_m1_e0 | * | 99.0258 | 99.1202 | 98.9317 | 67.1588 | 71766 | 637 | 71768 | 775 | 161 | 20.7742 | |
| ciseli-custom | SNP | * | map_l250_m0_e0 | het | 62.5646 | 57.7025 | 68.3215 | 96.1752 | 869 | 637 | 867 | 402 | 13 | 3.2338 | |
| ckim-isaac | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 96.6931 | 93.6813 | 99.9050 | 54.1997 | 9459 | 638 | 9468 | 9 | 7 | 77.7778 | |
| hfeng-pmm1 | INDEL | D1_5 | * | het | 99.5580 | 99.2715 | 99.8461 | 55.4481 | 86936 | 638 | 86940 | 134 | 51 | 38.0597 | |
| hfeng-pmm1 | INDEL | D6_15 | HG002compoundhet | * | 95.4940 | 92.9354 | 98.1974 | 32.8011 | 8393 | 638 | 8389 | 154 | 150 | 97.4026 | |
| rpoplin-dv42 | INDEL | D1_5 | HG002compoundhet | * | 95.7563 | 94.7855 | 96.7473 | 62.2778 | 11597 | 638 | 11600 | 390 | 380 | 97.4359 | |
| bgallagher-sentieon | INDEL | D1_5 | HG002compoundhet | * | 95.8155 | 94.7855 | 96.8682 | 66.0428 | 11597 | 638 | 11599 | 375 | 373 | 99.4667 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 77.8141 | 67.6306 | 91.6078 | 59.9900 | 1333 | 638 | 2205 | 202 | 194 | 96.0396 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 77.8141 | 67.6306 | 91.6078 | 59.9900 | 1333 | 638 | 2205 | 202 | 194 | 96.0396 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 0.4680 | 0.0000 | 0.0000 | 3 | 638 | 0 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | * | map_l100_m2_e0 | het | 83.4500 | 72.3450 | 98.5824 | 93.3707 | 1669 | 638 | 1669 | 24 | 8 | 33.3333 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 11.5234 | 8.4648 | 18.0428 | 48.1775 | 59 | 638 | 59 | 268 | 265 | 98.8806 | |
| ciseli-custom | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 86.4138 | 96.3627 | 78.3270 | 66.2442 | 16929 | 639 | 17004 | 4705 | 98 | 2.0829 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 83.5360 | 76.8142 | 91.5470 | 43.3092 | 2117 | 639 | 2296 | 212 | 212 | 100.0000 | |
| asubramanian-gatk | SNP | tv | map_l250_m0_e0 | * | 28.2828 | 16.4706 | 100.0000 | 99.1823 | 126 | 639 | 126 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.7498 | 97.1281 | 98.3795 | 53.6051 | 21611 | 639 | 21612 | 356 | 342 | 96.0674 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 73.0196 | 90.4177 | 61.2365 | 38.8818 | 6039 | 640 | 15303 | 9687 | 8838 | 91.2357 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 0.0000 | 19.1677 | 0.0000 | 0.0000 | 152 | 641 | 0 | 0 | 0 | ||
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 38.9035 | 36.0279 | 42.2780 | 67.7158 | 361 | 641 | 438 | 598 | 312 | 52.1739 | |
| ltrigg-rtg1 | INDEL | D1_5 | HG002compoundhet | * | 96.8842 | 94.7609 | 99.1047 | 63.0486 | 11594 | 641 | 11623 | 105 | 78 | 74.2857 | |
| raldana-dualsentieon | INDEL | D1_5 | * | het | 99.5220 | 99.2680 | 99.7773 | 56.3227 | 86933 | 641 | 86937 | 194 | 136 | 70.1031 | |
| jlack-gatk | SNP | * | map_l100_m1_e0 | * | 97.0238 | 99.1147 | 95.0193 | 74.0812 | 71762 | 641 | 71751 | 3761 | 290 | 7.7107 | |
| ckim-gatk | INDEL | D1_5 | HG002compoundhet | hetalt | 96.5709 | 93.7255 | 99.5943 | 58.2762 | 9575 | 641 | 9575 | 39 | 39 | 100.0000 | |
| cchapple-custom | SNP | ti | map_siren | homalt | 99.1409 | 98.3094 | 99.9866 | 47.3567 | 37275 | 641 | 37258 | 5 | 5 | 100.0000 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 73.4894 | 61.2085 | 91.9355 | 34.5468 | 1013 | 642 | 1653 | 145 | 143 | 98.6207 | |
| ckim-vqsr | INDEL | D1_5 | HG002compoundhet | hetalt | 96.5656 | 93.7157 | 99.5943 | 58.2787 | 9574 | 642 | 9574 | 39 | 39 | 100.0000 | |
| jpowers-varprowl | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.9005 | 98.1874 | 97.6153 | 68.2457 | 34777 | 642 | 34917 | 853 | 41 | 4.8066 | |
| ltrigg-rtg2 | INDEL | * | HG002complexvar | het | 99.0269 | 98.6108 | 99.4465 | 53.1360 | 45570 | 642 | 44739 | 249 | 116 | 46.5863 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.4896 | 97.3839 | 99.6207 | 39.3186 | 23898 | 642 | 23900 | 91 | 86 | 94.5055 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 88.2413 | 79.4231 | 99.2621 | 38.3627 | 2478 | 642 | 3094 | 23 | 17 | 73.9130 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 45.8754 | 35.9281 | 63.4398 | 55.1086 | 360 | 642 | 616 | 355 | 312 | 87.8873 | |
| gduggal-snapfb | SNP | ti | map_l125_m0_e0 | * | 95.4780 | 94.9616 | 96.0000 | 76.0355 | 12119 | 643 | 12120 | 505 | 265 | 52.4752 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 87.6160 | 82.5603 | 93.3313 | 53.0320 | 3044 | 643 | 3065 | 219 | 187 | 85.3881 | |