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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
69251-69300 / 86044 show all | |||||||||||||||
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 88.8708 | 82.4960 | 96.3134 | 28.0265 | 5632 | 1195 | 1672 | 64 | 39 | 60.9375 | |
| anovak-vg | SNP | tv | func_cds | homalt | 98.9685 | 98.7676 | 99.1701 | 25.0222 | 1683 | 21 | 1673 | 14 | 11 | 78.5714 | |
| ckim-isaac | SNP | tv | func_cds | homalt | 99.0820 | 98.1808 | 100.0000 | 21.0849 | 1673 | 31 | 1673 | 0 | 0 | ||
| ltrigg-rtg2 | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.3741 | 98.7559 | 100.0000 | 56.8481 | 1667 | 21 | 1673 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.2976 | 98.3558 | 98.2394 | 68.7282 | 1675 | 28 | 1674 | 30 | 5 | 16.6667 | |
| jlack-gatk | INDEL | D16_PLUS | * | homalt | 98.8194 | 98.9362 | 98.7028 | 69.0115 | 1674 | 18 | 1674 | 22 | 15 | 68.1818 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 45.4191 | 32.4145 | 75.8496 | 67.6203 | 1858 | 3874 | 1674 | 533 | 342 | 64.1651 | |
| gduggal-bwavard | SNP | tv | func_cds | homalt | 99.3503 | 98.7089 | 100.0000 | 25.9620 | 1682 | 22 | 1674 | 0 | 0 | ||
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.0254 | 98.4733 | 99.5838 | 72.6059 | 1677 | 26 | 1675 | 7 | 2 | 28.5714 | |
| ciseli-custom | INDEL | * | map_l100_m2_e1 | het | 73.2415 | 70.9774 | 75.6549 | 89.0075 | 1663 | 680 | 1675 | 539 | 319 | 59.1837 | |
| jli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9669 | 98.4733 | 99.4656 | 72.6845 | 1677 | 26 | 1675 | 9 | 2 | 22.2222 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.5561 | 93.3936 | 99.9404 | 41.2198 | 1654 | 117 | 1676 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.5561 | 93.3936 | 99.9404 | 41.4660 | 1654 | 117 | 1676 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | * | homalt | 99.2597 | 99.0544 | 99.4659 | 65.7799 | 1676 | 16 | 1676 | 9 | 4 | 44.4444 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.1143 | 98.5907 | 99.6435 | 73.6743 | 1679 | 24 | 1677 | 6 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | D16_PLUS | * | homalt | 99.0257 | 99.1135 | 98.9381 | 67.4789 | 1677 | 15 | 1677 | 18 | 12 | 66.6667 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.7441 | 95.6423 | 99.9404 | 50.0892 | 1690 | 77 | 1677 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.5585 | 93.4500 | 99.8809 | 40.1426 | 1655 | 116 | 1677 | 2 | 2 | 100.0000 | |
| qzeng-custom | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.2303 | 99.2299 | 99.2308 | 68.4878 | 1675 | 13 | 1677 | 13 | 7 | 53.8462 | |
| rpoplin-dv42 | INDEL | D1_5 | HG002compoundhet | het | 90.2551 | 96.8171 | 84.5262 | 76.1853 | 1673 | 55 | 1677 | 307 | 300 | 97.7199 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.1148 | 98.6494 | 99.5846 | 73.9124 | 1680 | 23 | 1678 | 7 | 2 | 28.5714 | |
| hfeng-pmm3 | INDEL | D16_PLUS | * | homalt | 99.3781 | 99.1726 | 99.5846 | 66.6072 | 1678 | 14 | 1678 | 7 | 4 | 57.1429 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 94.4937 | 90.2365 | 99.1726 | 34.9981 | 1488 | 161 | 1678 | 14 | 14 | 100.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.1148 | 98.6494 | 99.5846 | 74.0889 | 1680 | 23 | 1678 | 7 | 1 | 14.2857 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.9984 | 94.8103 | 99.2899 | 54.8611 | 1699 | 93 | 1678 | 12 | 9 | 75.0000 | |
| asubramanian-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.4640 | 98.9336 | 100.0000 | 64.4882 | 1670 | 18 | 1679 | 0 | 0 | ||
| astatham-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.7327 | 99.4668 | 100.0000 | 64.1699 | 1679 | 9 | 1679 | 0 | 0 | ||
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.7031 | 99.4668 | 99.9405 | 63.6364 | 1679 | 9 | 1679 | 1 | 1 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.1044 | 93.8977 | 98.4174 | 74.4802 | 1708 | 111 | 1679 | 27 | 14 | 51.8519 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.1044 | 93.8977 | 98.4174 | 74.4802 | 1708 | 111 | 1679 | 27 | 14 | 51.8519 | |
| jli-custom | INDEL | D16_PLUS | * | homalt | 99.0858 | 99.2908 | 98.8817 | 67.1754 | 1680 | 12 | 1680 | 19 | 13 | 68.4211 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.5238 | 99.0521 | 100.0000 | 59.3712 | 1672 | 16 | 1680 | 0 | 0 | ||
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 82.8529 | 82.0562 | 83.6653 | 62.9041 | 1724 | 377 | 1680 | 328 | 287 | 87.5000 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 47.7873 | 41.5540 | 56.2207 | 53.8295 | 1690 | 2377 | 1681 | 1309 | 1280 | 97.7846 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 47.6114 | 41.5540 | 55.7361 | 61.7356 | 1690 | 2377 | 1681 | 1335 | 1256 | 94.0824 | |
| cchapple-custom | INDEL | * | segdup | het | 99.0552 | 98.7040 | 99.4090 | 95.0259 | 1447 | 19 | 1682 | 10 | 3 | 30.0000 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.1384 | 90.5537 | 98.0186 | 60.1764 | 1668 | 174 | 1682 | 34 | 29 | 85.2941 | |
| ckim-dragen | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.6736 | 99.4668 | 99.8812 | 64.0938 | 1679 | 9 | 1682 | 2 | 2 | 100.0000 | |
| anovak-vg | INDEL | * | map_l125_m2_e0 | * | 72.8494 | 74.4991 | 71.2712 | 87.8407 | 1636 | 560 | 1682 | 678 | 383 | 56.4897 | |
| rpoplin-dv42 | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.7923 | 99.6445 | 99.9406 | 65.1625 | 1682 | 6 | 1682 | 1 | 1 | 100.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.8220 | 99.6445 | 100.0000 | 64.1135 | 1682 | 6 | 1682 | 0 | 0 | ||
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 78.6349 | 78.0148 | 79.2648 | 83.6794 | 1682 | 474 | 1682 | 440 | 405 | 92.0455 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9127 | 98.8843 | 98.9412 | 74.7999 | 1684 | 19 | 1682 | 18 | 4 | 22.2222 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.2044 | 98.8843 | 99.5266 | 75.4930 | 1684 | 19 | 1682 | 8 | 1 | 12.5000 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.8238 | 92.6407 | 99.2335 | 33.1757 | 1498 | 119 | 1683 | 13 | 13 | 100.0000 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 93.4647 | 97.8852 | 89.4261 | 56.5157 | 1620 | 35 | 1683 | 199 | 186 | 93.4673 | |
| ckim-dragen | INDEL | D16_PLUS | * | homalt | 97.0588 | 99.4681 | 94.7635 | 72.2066 | 1683 | 9 | 1683 | 93 | 84 | 90.3226 | |
| ckim-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.8814 | 99.7630 | 100.0000 | 64.0862 | 1684 | 4 | 1684 | 0 | 0 | ||
| dgrover-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.8814 | 99.7630 | 100.0000 | 64.2235 | 1684 | 4 | 1684 | 0 | 0 | ||
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.4511 | 98.9430 | 97.9639 | 73.8833 | 1685 | 18 | 1684 | 35 | 28 | 80.0000 | |