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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
71901-71950 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.5108 | 94.0299 | 99.1263 | 61.5359 | 2268 | 144 | 2269 | 20 | 15 | 75.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 82.8480 | 83.5616 | 82.1464 | 73.3422 | 732 | 144 | 819 | 178 | 170 | 95.5056 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 94.0820 | 92.6941 | 95.5121 | 71.6510 | 1827 | 144 | 1809 | 85 | 58 | 68.2353 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 94.0820 | 92.6941 | 95.5121 | 71.6510 | 1827 | 144 | 1809 | 85 | 58 | 68.2353 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.5233 | 95.1335 | 95.9163 | 58.0490 | 2815 | 144 | 2842 | 121 | 62 | 51.2397 | |
| astatham-gatk | SNP | ti | map_l250_m0_e0 | * | 93.8385 | 89.4891 | 98.6323 | 93.8175 | 1226 | 144 | 1226 | 17 | 3 | 17.6471 | |
| astatham-gatk | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.1948 | 98.5039 | 99.8954 | 68.1029 | 9547 | 145 | 9547 | 10 | 9 | 90.0000 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 97.8222 | 97.8503 | 97.7942 | 34.8099 | 6600 | 145 | 6606 | 149 | 125 | 83.8926 | |
| bgallagher-sentieon | SNP | * | map_l100_m0_e0 | het | 98.8545 | 99.3162 | 98.3971 | 73.2385 | 21060 | 145 | 21056 | 343 | 49 | 14.2857 | |
| bgallagher-sentieon | SNP | * | map_l150_m1_e0 | het | 98.7760 | 99.2493 | 98.3073 | 78.6499 | 19171 | 145 | 19165 | 330 | 49 | 14.8485 | |
| bgallagher-sentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.3414 | 99.5344 | 99.1492 | 66.7959 | 30998 | 145 | 30998 | 266 | 16 | 6.0150 | |
| bgallagher-sentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.3414 | 99.5344 | 99.1492 | 66.7959 | 30998 | 145 | 30998 | 266 | 16 | 6.0150 | |
| bgallagher-sentieon | SNP | ti | map_l100_m0_e0 | * | 99.2132 | 99.3340 | 99.0926 | 69.0197 | 21626 | 145 | 21623 | 198 | 35 | 17.6768 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 90.9078 | 83.8350 | 99.2840 | 42.0470 | 752 | 145 | 832 | 6 | 5 | 83.3333 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 45.9328 | 83.4475 | 31.6874 | 62.3505 | 731 | 145 | 738 | 1591 | 1584 | 99.5600 | |
| jli-custom | INDEL | I16_PLUS | HG002compoundhet | * | 95.4155 | 93.2338 | 97.7017 | 49.8529 | 1998 | 145 | 1998 | 47 | 42 | 89.3617 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.5563 | 99.1458 | 99.9703 | 67.1493 | 16830 | 145 | 16830 | 5 | 5 | 100.0000 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.5563 | 99.1458 | 99.9703 | 67.1493 | 16830 | 145 | 16830 | 5 | 5 | 100.0000 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.3339 | 96.4347 | 96.2334 | 71.2425 | 3922 | 145 | 3909 | 153 | 129 | 84.3137 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 91.2068 | 83.8350 | 100.0000 | 41.5864 | 752 | 145 | 788 | 0 | 0 | ||
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 77.3509 | 67.3423 | 90.8537 | 63.9164 | 299 | 145 | 298 | 30 | 27 | 90.0000 | |
| ciseli-custom | INDEL | I1_5 | map_l150_m1_e0 | homalt | 41.0416 | 26.7677 | 87.9310 | 92.1196 | 53 | 145 | 51 | 7 | 4 | 57.1429 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 36.5732 | 34.6847 | 38.6792 | 60.6679 | 77 | 145 | 82 | 130 | 106 | 81.5385 | |
| rpoplin-dv42 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.5123 | 99.4950 | 99.5296 | 71.9110 | 28567 | 145 | 28561 | 135 | 47 | 34.8148 | |
| rpoplin-dv42 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.5123 | 99.4950 | 99.5296 | 71.9110 | 28567 | 145 | 28561 | 135 | 47 | 34.8148 | |
| rpoplin-dv42 | SNP | * | map_l100_m2_e1 | homalt | 99.6343 | 99.4783 | 99.7907 | 63.6404 | 27651 | 145 | 27652 | 58 | 54 | 93.1034 | |
| raldana-dualsentieon | SNP | * | map_l250_m2_e0 | * | 98.1797 | 98.1611 | 98.1984 | 88.2926 | 7740 | 145 | 7740 | 142 | 6 | 4.2254 | |
| qzeng-custom | INDEL | * | map_l150_m2_e0 | homalt | 81.0641 | 69.8545 | 96.5591 | 89.8494 | 336 | 145 | 449 | 16 | 9 | 56.2500 | |
| qzeng-custom | INDEL | * | map_l150_m2_e1 | homalt | 81.5445 | 70.5285 | 96.6387 | 89.8225 | 347 | 145 | 460 | 16 | 9 | 56.2500 | |
| ltrigg-rtg2 | INDEL | I1_5 | HG002complexvar | het | 99.3853 | 99.2028 | 99.5685 | 52.2881 | 18044 | 145 | 17305 | 75 | 44 | 58.6667 | |
| ltrigg-rtg2 | SNP | * | HG002compoundhet | het | 99.2921 | 98.9773 | 99.6090 | 42.0270 | 14033 | 145 | 14011 | 55 | 13 | 23.6364 | |
| qzeng-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.1549 | 98.4124 | 93.9987 | 87.3444 | 8988 | 145 | 9022 | 576 | 32 | 5.5556 | |
| qzeng-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.1549 | 98.4124 | 93.9987 | 87.3444 | 8988 | 145 | 9022 | 576 | 32 | 5.5556 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 64.4614 | 84.9116 | 51.9498 | 59.0528 | 816 | 145 | 786 | 727 | 719 | 98.8996 | |
| hfeng-pmm1 | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.5502 | 99.2026 | 99.9003 | 37.1632 | 18038 | 145 | 18035 | 18 | 3 | 16.6667 | |
| hfeng-pmm1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 93.9208 | 88.8117 | 99.6537 | 86.9255 | 1151 | 145 | 1151 | 4 | 0 | 0.0000 | |
| jlack-gatk | SNP | tv | map_l150_m1_e0 | * | 94.3885 | 98.6712 | 90.4622 | 83.2378 | 10767 | 145 | 10765 | 1135 | 67 | 5.9031 | |
| egarrison-hhga | SNP | * | map_l250_m2_e1 | het | 98.3289 | 97.2454 | 99.4367 | 88.6583 | 5119 | 145 | 5119 | 29 | 11 | 37.9310 | |
| egarrison-hhga | SNP | tv | HG002compoundhet | het | 98.2001 | 96.8971 | 99.5386 | 52.4849 | 4528 | 145 | 4530 | 21 | 10 | 47.6190 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.5470 | 99.1558 | 99.9413 | 57.3410 | 17032 | 145 | 17028 | 10 | 8 | 80.0000 | |
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 96.3741 | 93.2180 | 99.7514 | 32.0838 | 1993 | 145 | 2006 | 5 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6915 | 99.4869 | 99.8970 | 58.9754 | 28115 | 145 | 28118 | 29 | 17 | 58.6207 | |
| dgrover-gatk | SNP | * | map_l150_m0_e0 | * | 98.7537 | 98.7949 | 98.7125 | 82.2666 | 11887 | 145 | 11884 | 155 | 29 | 18.7097 | |
| gduggal-snapplat | INDEL | * | map_l150_m0_e0 | * | 78.7001 | 71.7899 | 87.0824 | 96.1959 | 369 | 145 | 391 | 58 | 10 | 17.2414 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 92.7794 | 95.0997 | 90.5697 | 78.5117 | 2814 | 145 | 2814 | 293 | 6 | 2.0478 | |
| gduggal-bwafb | SNP | ti | map_l150_m0_e0 | * | 98.4686 | 98.1555 | 98.7838 | 81.2749 | 7716 | 145 | 7716 | 95 | 36 | 37.8947 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 75.8730 | 62.2396 | 97.1545 | 85.6476 | 239 | 145 | 239 | 7 | 1 | 14.2857 | |
| eyeh-varpipe | INDEL | D16_PLUS | HG002complexvar | homalt | 44.7304 | 49.8270 | 40.5797 | 45.3249 | 144 | 145 | 140 | 205 | 205 | 100.0000 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 78.3674 | 76.9841 | 79.8013 | 72.5330 | 485 | 145 | 482 | 122 | 85 | 69.6721 | |
| eyeh-varpipe | INDEL | D1_5 | HG002compoundhet | het | 84.7249 | 91.5509 | 78.8462 | 70.2988 | 1582 | 146 | 533 | 143 | 97 | 67.8322 | |