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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
63851-63900 / 86044 show all | |||||||||||||||
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 63.0461 | 57.4841 | 69.7998 | 69.3027 | 722 | 534 | 802 | 347 | 171 | 49.2795 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 97.5041 | 98.4993 | 96.5287 | 73.6731 | 722 | 11 | 723 | 26 | 13 | 50.0000 | |
| ckim-gatk | SNP | * | map_l250_m0_e0 | het | 63.7809 | 47.9416 | 95.2507 | 98.3918 | 722 | 784 | 722 | 36 | 2 | 5.5556 | |
| gduggal-snapplat | INDEL | * | segdup | homalt | 82.9294 | 75.2083 | 92.4171 | 94.6528 | 722 | 238 | 780 | 64 | 13 | 20.3125 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 91.5095 | 84.7418 | 99.4521 | 75.3295 | 722 | 130 | 726 | 4 | 4 | 100.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 91.6849 | 87.6214 | 96.1436 | 66.2478 | 722 | 102 | 723 | 29 | 8 | 27.5862 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.8600 | 97.3046 | 98.4218 | 73.5584 | 722 | 20 | 686 | 11 | 5 | 45.4545 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 76.5556 | 82.5342 | 71.3846 | 62.2751 | 723 | 153 | 464 | 186 | 158 | 84.9462 | |
| egarrison-hhga | INDEL | * | map_l125_m1_e0 | homalt | 98.9056 | 98.7705 | 99.0411 | 85.3443 | 723 | 9 | 723 | 7 | 4 | 57.1429 | |
| anovak-vg | INDEL | D1_5 | map_l100_m0_e0 | * | 82.9849 | 83.7775 | 82.2072 | 86.7066 | 723 | 140 | 730 | 158 | 62 | 39.2405 | |
| astatham-gatk | INDEL | D1_5 | map_l125_m2_e0 | het | 95.7656 | 94.6335 | 96.9251 | 88.4193 | 723 | 41 | 725 | 23 | 3 | 13.0435 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.7912 | 97.4394 | 98.1455 | 73.7551 | 723 | 19 | 688 | 13 | 9 | 69.2308 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 89.1544 | 80.6020 | 99.7372 | 41.6858 | 723 | 174 | 759 | 2 | 2 | 100.0000 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.4343 | 98.6357 | 98.2337 | 71.3284 | 723 | 10 | 723 | 13 | 9 | 69.2308 | |
| gduggal-snapvard | SNP | tv | map_l250_m0_e0 | * | 78.0985 | 94.5098 | 66.5434 | 94.1611 | 723 | 42 | 720 | 362 | 4 | 1.1050 | |
| cchapple-custom | SNP | tv | map_l250_m0_e0 | * | 94.5681 | 94.5098 | 94.6265 | 93.8008 | 723 | 42 | 722 | 41 | 8 | 19.5122 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.9984 | 97.5741 | 98.4263 | 73.5027 | 724 | 18 | 688 | 11 | 5 | 45.4545 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 97.6456 | 96.2766 | 99.0541 | 57.2748 | 724 | 28 | 733 | 7 | 7 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D1_5 | map_l150_m2_e0 | * | 97.0527 | 94.8886 | 99.3179 | 83.4836 | 724 | 39 | 728 | 5 | 2 | 40.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.9984 | 97.5741 | 98.4263 | 73.4018 | 724 | 18 | 688 | 11 | 5 | 45.4545 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.9298 | 97.5741 | 98.2882 | 73.1623 | 724 | 18 | 689 | 12 | 6 | 50.0000 | |
| dgrover-gatk | INDEL | * | map_l125_m1_e0 | homalt | 98.9747 | 98.9071 | 99.0424 | 86.2723 | 724 | 8 | 724 | 7 | 4 | 57.1429 | |
| rpoplin-dv42 | INDEL | * | map_l125_m1_e0 | homalt | 98.9747 | 98.9071 | 99.0424 | 85.2054 | 724 | 8 | 724 | 7 | 6 | 85.7143 | |
| gduggal-snapfb | SNP | tv | map_l250_m0_e0 | * | 93.9650 | 94.6405 | 93.2990 | 94.3329 | 724 | 41 | 724 | 52 | 12 | 23.0769 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.9071 | 98.7722 | 99.0424 | 71.9709 | 724 | 9 | 724 | 7 | 5 | 71.4286 | |
| gduggal-snapvard | INDEL | I1_5 | HG002complexvar | hetalt | 0.0000 | 41.9710 | 0.0000 | 0.0000 | 724 | 1001 | 0 | 0 | 0 | ||
| mlin-fermikit | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 56.8303 | 39.7366 | 99.7333 | 37.6559 | 724 | 1098 | 748 | 2 | 2 | 100.0000 | |
| jlack-gatk | INDEL | * | map_l125_m1_e0 | homalt | 98.9071 | 98.9071 | 98.9071 | 85.4009 | 724 | 8 | 724 | 8 | 4 | 50.0000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.6376 | 98.7722 | 98.5034 | 72.1591 | 724 | 9 | 724 | 11 | 7 | 63.6364 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.1114 | 98.9086 | 99.3151 | 72.3170 | 725 | 8 | 725 | 5 | 5 | 100.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.0674 | 97.7089 | 98.4286 | 73.8024 | 725 | 17 | 689 | 11 | 5 | 45.4545 | |
| ltrigg-rtg1 | INDEL | D1_5 | map_l125_m2_e1 | het | 96.6680 | 94.1558 | 99.3179 | 76.7302 | 725 | 45 | 728 | 5 | 0 | 0.0000 | |
| jpowers-varprowl | INDEL | I1_5 | map_l100_m1_e0 | het | 94.1526 | 93.3076 | 95.0131 | 86.3196 | 725 | 52 | 724 | 38 | 26 | 68.4211 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.3524 | 95.1444 | 95.5614 | 69.5669 | 725 | 37 | 732 | 34 | 14 | 41.1765 | |
| ndellapenna-hhga | INDEL | * | map_l125_m1_e0 | homalt | 98.9761 | 99.0437 | 98.9086 | 84.6202 | 725 | 7 | 725 | 8 | 6 | 75.0000 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 90.6252 | 83.1422 | 99.5885 | 23.9833 | 725 | 147 | 726 | 3 | 3 | 100.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 89.1786 | 80.8250 | 99.4580 | 43.1871 | 725 | 172 | 734 | 4 | 4 | 100.0000 | |
| ghariani-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 66.4821 | 91.3098 | 52.2696 | 87.6612 | 725 | 69 | 760 | 694 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | I1_5 | HG002complexvar | hetalt | 55.6197 | 42.0046 | 82.2940 | 85.5161 | 725 | 1001 | 739 | 159 | 112 | 70.4403 | |
| gduggal-snapplat | SNP | ti | map_l250_m0_e0 | het | 84.2801 | 77.7302 | 92.0354 | 96.9671 | 726 | 208 | 728 | 63 | 27 | 42.8571 | |
| gduggal-snapplat | SNP | tv | map_l250_m2_e0 | homalt | 87.3121 | 77.4813 | 100.0000 | 90.2170 | 726 | 211 | 726 | 0 | 0 | ||
| ltrigg-rtg1 | INDEL | * | map_l125_m1_e0 | homalt | 99.2467 | 99.1803 | 99.3132 | 84.0316 | 726 | 6 | 723 | 5 | 3 | 60.0000 | |
| jpowers-varprowl | INDEL | D1_5 | map_l150_m2_e1 | * | 93.7984 | 93.3162 | 94.2857 | 89.3910 | 726 | 52 | 726 | 44 | 22 | 50.0000 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.5075 | 99.0450 | 97.9757 | 72.8173 | 726 | 7 | 726 | 15 | 12 | 80.0000 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.2974 | 99.0450 | 97.5610 | 73.6240 | 726 | 7 | 720 | 18 | 14 | 77.7778 | |
| ckim-gatk | INDEL | * | map_l125_m1_e0 | homalt | 99.1803 | 99.1803 | 99.1803 | 86.4895 | 726 | 6 | 726 | 6 | 4 | 66.6667 | |
| ckim-vqsr | INDEL | * | map_l125_m1_e0 | homalt | 99.2481 | 99.1803 | 99.3160 | 86.5054 | 726 | 6 | 726 | 5 | 3 | 60.0000 | |
| gduggal-bwavard | INDEL | * | map_l125_m2_e1 | homalt | 96.3491 | 93.7984 | 99.0424 | 81.2275 | 726 | 48 | 724 | 7 | 4 | 57.1429 | |
| mlin-fermikit | INDEL | * | map_l125_m2_e0 | het | 67.2880 | 52.1927 | 94.6684 | 82.7849 | 726 | 665 | 728 | 41 | 17 | 41.4634 | |
| hfeng-pmm1 | INDEL | * | map_l125_m1_e0 | homalt | 99.2491 | 99.3169 | 99.1814 | 84.1205 | 727 | 5 | 727 | 6 | 3 | 50.0000 | |