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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
69351-69400 / 86044 show all | |||||||||||||||
| gduggal-bwafb | INDEL | D1_5 | map_siren | het | 98.2729 | 98.2872 | 98.2586 | 80.4710 | 2238 | 39 | 2257 | 40 | 2 | 5.0000 | |
| gduggal-bwavard | SNP | * | HG002complexvar | het | 98.2730 | 97.3044 | 99.2610 | 20.1947 | 452952 | 12548 | 441659 | 3288 | 2162 | 65.7543 | |
| hfeng-pmm3 | INDEL | * | map_l125_m2_e0 | het | 98.2731 | 98.0590 | 98.4881 | 86.4620 | 1364 | 27 | 1368 | 21 | 3 | 14.2857 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.2738 | 99.4197 | 97.1540 | 68.7190 | 3255 | 19 | 3243 | 95 | 92 | 96.8421 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.2739 | 96.9720 | 99.6112 | 61.8511 | 1281 | 40 | 1281 | 5 | 3 | 60.0000 | |
| anovak-vg | SNP | tv | func_cds | * | 98.2741 | 97.7580 | 98.7957 | 36.4158 | 4273 | 98 | 4266 | 52 | 32 | 61.5385 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l125_m0_e0 | het | 98.2742 | 98.8406 | 97.7143 | 86.4341 | 341 | 4 | 342 | 8 | 1 | 12.5000 | |
| ckim-vqsr | SNP | * | HG002complexvar | homalt | 98.2744 | 96.6168 | 99.9900 | 20.3688 | 278811 | 9763 | 278787 | 28 | 26 | 92.8571 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.2746 | 98.1228 | 98.4270 | 77.7694 | 92676 | 1773 | 96110 | 1536 | 892 | 58.0729 | |
| eyeh-varpipe | SNP | tv | map_l250_m2_e1 | het | 98.2749 | 99.5420 | 97.0396 | 91.1568 | 1956 | 9 | 1934 | 59 | 4 | 6.7797 | |
| hfeng-pmm3 | INDEL | * | map_l100_m0_e0 | * | 98.2754 | 98.3365 | 98.2143 | 84.4120 | 1537 | 26 | 1540 | 28 | 6 | 21.4286 | |
| jli-custom | INDEL | D6_15 | map_l125_m1_e0 | * | 98.2759 | 97.4359 | 99.1304 | 88.8781 | 114 | 3 | 114 | 1 | 0 | 0.0000 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.2759 | 96.6102 | 100.0000 | 70.4663 | 171 | 6 | 171 | 0 | 0 | ||
| jlack-gatk | INDEL | I1_5 | map_l125_m0_e0 | homalt | 98.2759 | 100.0000 | 96.6102 | 85.5037 | 114 | 0 | 114 | 4 | 2 | 50.0000 | |
| hfeng-pmm2 | INDEL | * | map_l250_m2_e1 | homalt | 98.2759 | 98.2759 | 98.2759 | 94.8444 | 114 | 2 | 114 | 2 | 2 | 100.0000 | |
| rpoplin-dv42 | INDEL | D6_15 | map_l125_m1_e0 | * | 98.2759 | 97.4359 | 99.1304 | 90.1457 | 114 | 3 | 114 | 1 | 0 | 0.0000 | |
| rpoplin-dv42 | SNP | ti | map_siren | hetalt | 98.2759 | 100.0000 | 96.6102 | 78.7004 | 57 | 0 | 57 | 2 | 2 | 100.0000 | |
| ckim-dragen | SNP | ti | map_siren | hetalt | 98.2759 | 100.0000 | 96.6102 | 72.1698 | 57 | 0 | 57 | 2 | 2 | 100.0000 | |
| ckim-gatk | INDEL | * | map_l250_m2_e1 | homalt | 98.2759 | 98.2759 | 98.2759 | 95.7196 | 114 | 2 | 114 | 2 | 2 | 100.0000 | |
| ltrigg-rtg1 | SNP | ti | map_siren | hetalt | 98.2759 | 100.0000 | 96.6102 | 66.2857 | 57 | 0 | 57 | 2 | 2 | 100.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | HG002complexvar | het | 98.2761 | 98.7353 | 97.8211 | 68.7119 | 1093 | 14 | 853 | 19 | 9 | 47.3684 | |
| anovak-vg | SNP | ti | HG002complexvar | homalt | 98.2762 | 97.3918 | 99.1768 | 17.9619 | 188418 | 5046 | 185045 | 1536 | 1381 | 89.9089 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 98.2763 | 96.9365 | 99.6537 | 46.3792 | 2563 | 81 | 2590 | 9 | 8 | 88.8889 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.2766 | 99.2360 | 97.3356 | 73.4116 | 1169 | 9 | 1169 | 32 | 32 | 100.0000 | |
| hfeng-pmm3 | INDEL | * | map_l125_m1_e0 | het | 98.2769 | 98.1273 | 98.4270 | 85.5800 | 1310 | 25 | 1314 | 21 | 3 | 14.2857 | |
| gduggal-snapfb | INDEL | D1_5 | map_l125_m1_e0 | homalt | 98.2779 | 97.9943 | 98.5632 | 89.1589 | 342 | 7 | 343 | 5 | 3 | 60.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.2781 | 97.3753 | 99.1979 | 63.8123 | 742 | 20 | 742 | 6 | 1 | 16.6667 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.2782 | 97.1365 | 99.4471 | 33.4959 | 10109 | 298 | 17626 | 98 | 90 | 91.8367 | |
| cchapple-custom | INDEL | * | map_l125_m2_e0 | homalt | 98.2786 | 97.2477 | 99.3316 | 84.9709 | 742 | 21 | 743 | 5 | 4 | 80.0000 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.2792 | 97.5341 | 99.0358 | 68.7742 | 1503 | 38 | 1438 | 14 | 3 | 21.4286 | |
| gduggal-snapvard | SNP | * | segdup | * | 98.2794 | 97.3955 | 99.1795 | 93.1728 | 27336 | 731 | 27076 | 224 | 72 | 32.1429 | |
| bgallagher-sentieon | SNP | * | map_l150_m0_e0 | het | 98.2803 | 98.9924 | 97.5782 | 83.1442 | 7860 | 80 | 7857 | 195 | 22 | 11.2821 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.2804 | 98.3316 | 98.2292 | 73.6842 | 943 | 16 | 943 | 17 | 11 | 64.7059 | |
| ghariani-varprowl | SNP | ti | map_l250_m2_e1 | homalt | 98.2808 | 96.7833 | 99.8254 | 88.3683 | 1715 | 57 | 1715 | 3 | 3 | 100.0000 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.2808 | 99.8350 | 96.7742 | 42.6049 | 18153 | 30 | 18150 | 605 | 8 | 1.3223 | |
| jpowers-varprowl | SNP | ti | map_l250_m2_e1 | homalt | 98.2808 | 96.7833 | 99.8254 | 89.5879 | 1715 | 57 | 1715 | 3 | 3 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | * | * | 98.2810 | 97.0642 | 99.5288 | 47.5098 | 25326 | 766 | 25133 | 119 | 76 | 63.8655 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.2812 | 96.8927 | 99.7101 | 66.5373 | 343 | 11 | 344 | 1 | 1 | 100.0000 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.2813 | 99.4514 | 97.1385 | 53.8661 | 11421 | 63 | 11406 | 336 | 321 | 95.5357 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.2818 | 98.6207 | 97.9452 | 69.3920 | 429 | 6 | 429 | 9 | 4 | 44.4444 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.2818 | 96.6216 | 100.0000 | 72.0930 | 429 | 15 | 420 | 0 | 0 | ||
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.2824 | 98.0398 | 98.5261 | 67.2886 | 64070 | 1281 | 63840 | 955 | 849 | 88.9005 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.2824 | 98.0398 | 98.5261 | 67.2886 | 64070 | 1281 | 63840 | 955 | 849 | 88.9005 | |
| qzeng-custom | SNP | * | HG002compoundhet | * | 98.2824 | 98.1489 | 98.4164 | 46.9711 | 25344 | 478 | 25604 | 412 | 148 | 35.9223 | |
| ckim-dragen | INDEL | I1_5 | map_l150_m2_e1 | homalt | 98.2837 | 98.5294 | 98.0392 | 87.7182 | 201 | 3 | 200 | 4 | 3 | 75.0000 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.2837 | 99.7301 | 96.8787 | 61.7262 | 11453 | 31 | 11453 | 369 | 356 | 96.4770 | |
| ltrigg-rtg2 | SNP | * | map_l125_m0_e0 | * | 98.2838 | 96.7501 | 99.8669 | 59.4717 | 18755 | 630 | 18753 | 25 | 4 | 16.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | * | homalt | 98.2839 | 99.5993 | 97.0028 | 48.9358 | 6214 | 25 | 6214 | 192 | 191 | 99.4792 | |
| ckim-dragen | SNP | * | map_l100_m0_e0 | * | 98.2840 | 98.9495 | 97.6275 | 70.9502 | 32496 | 345 | 32508 | 790 | 91 | 11.5190 | |
| jli-custom | INDEL | D1_5 | map_l150_m2_e1 | het | 98.2844 | 98.6590 | 97.9127 | 88.3097 | 515 | 7 | 516 | 11 | 3 | 27.2727 | |