PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
10101-10150 / 86044 show all | |||||||||||||||
| anovak-vg | INDEL | C1_5 | HG002complexvar | het | 55.6456 | 71.4286 | 45.5752 | 82.8658 | 5 | 2 | 103 | 123 | 15 | 12.1951 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 35.0904 | 39.3443 | 31.6667 | 53.3679 | 48 | 74 | 57 | 123 | 84 | 68.2927 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.2810 | 93.7940 | 96.8159 | 46.5107 | 2796 | 185 | 3740 | 123 | 114 | 92.6829 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 49.9912 | 39.7086 | 67.4603 | 80.7634 | 218 | 331 | 255 | 123 | 24 | 19.5122 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 83.9922 | 90.3153 | 78.4965 | 79.8804 | 401 | 43 | 449 | 123 | 104 | 84.5528 | |
| bgallagher-sentieon | INDEL | D16_PLUS | * | het | 97.5876 | 99.3036 | 95.9298 | 78.0298 | 3137 | 22 | 2899 | 123 | 76 | 61.7886 | |
| bgallagher-sentieon | INDEL | D1_5 | HG002compoundhet | het | 95.8083 | 98.4954 | 93.2640 | 79.3041 | 1702 | 26 | 1703 | 123 | 122 | 99.1870 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 89.1674 | 84.1986 | 94.7593 | 66.6240 | 2238 | 420 | 2224 | 123 | 104 | 84.5528 | |
| jpowers-varprowl | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.4333 | 99.6568 | 93.4119 | 74.1305 | 1742 | 6 | 1744 | 123 | 51 | 41.4634 | |
| jli-custom | SNP | ti | segdup | het | 99.4165 | 99.8504 | 98.9864 | 89.3080 | 12012 | 18 | 12012 | 123 | 2 | 1.6260 | |
| jli-custom | INDEL | D1_5 | * | het | 99.7840 | 99.7088 | 99.8593 | 56.7542 | 87319 | 255 | 87313 | 123 | 65 | 52.8455 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.4351 | 94.7749 | 98.1545 | 42.9464 | 6548 | 361 | 6542 | 123 | 88 | 71.5447 | |
| egarrison-hhga | SNP | ti | map_siren | * | 99.6715 | 99.4669 | 99.8769 | 52.8764 | 99820 | 535 | 99821 | 123 | 54 | 43.9024 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 92.1781 | 91.6618 | 92.7003 | 64.7784 | 1561 | 142 | 1562 | 123 | 54 | 43.9024 | |
| dgrover-gatk | SNP | ti | map_l125_m0_e0 | * | 99.0401 | 99.0440 | 99.0361 | 76.9678 | 12640 | 122 | 12638 | 123 | 30 | 24.3902 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.7824 | 99.8573 | 95.7920 | 54.8083 | 2800 | 4 | 2800 | 123 | 122 | 99.1870 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 93.7883 | 91.0957 | 96.6448 | 54.7687 | 3550 | 347 | 3543 | 123 | 90 | 73.1707 | |
| raldana-dualsentieon | INDEL | * | HG002complexvar | homalt | 99.7249 | 99.9038 | 99.5467 | 56.9673 | 27001 | 26 | 27010 | 123 | 119 | 96.7480 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 62.9507 | 62.6214 | 63.2836 | 70.3802 | 129 | 77 | 212 | 123 | 48 | 39.0244 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m0_e0 | het | 89.8148 | 98.4772 | 82.5532 | 89.6186 | 582 | 9 | 582 | 123 | 22 | 17.8862 | |
| ckim-dragen | INDEL | * | map_l100_m1_e0 | * | 96.9560 | 97.3229 | 96.5919 | 86.1888 | 3490 | 96 | 3486 | 123 | 19 | 15.4472 | |
| ckim-dragen | INDEL | D16_PLUS | HG002compoundhet | * | 94.5882 | 94.4468 | 94.7301 | 35.7379 | 2211 | 130 | 2211 | 123 | 120 | 97.5610 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 88.4335 | 83.8126 | 93.5937 | 65.9030 | 1807 | 349 | 1797 | 123 | 60 | 48.7805 | |
| cchapple-custom | SNP | * | HG002compoundhet | het | 98.9809 | 98.7163 | 99.2469 | 44.7646 | 13996 | 182 | 16209 | 123 | 92 | 74.7967 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.5003 | 95.5391 | 97.4811 | 71.7827 | 4776 | 223 | 4760 | 123 | 101 | 82.1138 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.5003 | 95.5391 | 97.4811 | 71.7827 | 4776 | 223 | 4760 | 123 | 101 | 82.1138 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.3211 | 96.1768 | 98.4930 | 60.0607 | 8075 | 321 | 8039 | 123 | 117 | 95.1220 | |
| gduggal-snapfb | INDEL | * | segdup | * | 93.0343 | 91.0407 | 95.1171 | 94.2770 | 2327 | 229 | 2396 | 123 | 43 | 34.9593 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 87.7617 | 87.8607 | 87.6630 | 63.7323 | 883 | 122 | 874 | 123 | 103 | 83.7398 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 83.6479 | 73.1252 | 97.7082 | 43.0315 | 5246 | 1928 | 5244 | 123 | 121 | 98.3740 | |
| gduggal-bwaplat | INDEL | I6_15 | * | homalt | 91.2395 | 85.5426 | 97.7493 | 57.4509 | 5337 | 902 | 5342 | 123 | 103 | 83.7398 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 83.7908 | 73.3408 | 97.7136 | 42.2636 | 5216 | 1896 | 5214 | 122 | 120 | 98.3607 | |
| 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 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 82.9234 | 95.9538 | 73.0088 | 76.1352 | 332 | 14 | 330 | 122 | 85 | 69.6721 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 86.3098 | 85.7592 | 86.8676 | 76.1917 | 819 | 136 | 807 | 122 | 105 | 86.0656 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 89.6122 | 99.4536 | 81.5431 | 79.4401 | 546 | 3 | 539 | 122 | 105 | 86.0656 | |
| gduggal-bwavard | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.9684 | 95.8443 | 92.1644 | 78.1320 | 1453 | 63 | 1435 | 122 | 17 | 13.9344 | |
| qzeng-custom | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 97.6562 | 98.9840 | 96.3636 | 77.0001 | 3215 | 33 | 3233 | 122 | 9 | 7.3771 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.1456 | 97.0290 | 99.2882 | 49.3199 | 17146 | 525 | 17018 | 122 | 80 | 65.5738 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.1456 | 97.0290 | 99.2882 | 49.3199 | 17146 | 525 | 17018 | 122 | 80 | 65.5738 | |
| ltrigg-rtg2 | SNP | tv | segdup | het | 98.5667 | 99.4137 | 97.7340 | 87.6779 | 5256 | 31 | 5262 | 122 | 2 | 1.6393 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 23.0412 | 16.2978 | 39.3035 | 77.1850 | 81 | 416 | 79 | 122 | 119 | 97.5410 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.6651 | 96.3610 | 96.9712 | 69.6092 | 3919 | 148 | 3906 | 122 | 111 | 90.9836 | |
| ltrigg-rtg1 | INDEL | I6_15 | * | * | 97.4037 | 95.4115 | 99.4808 | 44.5038 | 23684 | 1139 | 23374 | 122 | 76 | 62.2951 | |
| ltrigg-rtg1 | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.5720 | 99.5845 | 99.5594 | 59.6473 | 27563 | 115 | 27568 | 122 | 11 | 9.0164 | |
| jlack-gatk | INDEL | D1_5 | map_l125_m1_e0 | het | 91.7875 | 99.0358 | 85.5279 | 90.3635 | 719 | 7 | 721 | 122 | 5 | 4.0984 | |
| hfeng-pmm2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.6105 | 97.8651 | 99.3674 | 66.4258 | 19161 | 418 | 19162 | 122 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.6105 | 97.8651 | 99.3674 | 66.4258 | 19161 | 418 | 19162 | 122 | 0 | 0.0000 | |
| hfeng-pmm3 | SNP | * | map_l150_m1_e0 | het | 99.2744 | 99.1820 | 99.3670 | 75.4908 | 19158 | 158 | 19152 | 122 | 13 | 10.6557 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.7841 | 96.1888 | 99.4332 | 49.3970 | 21402 | 848 | 21403 | 122 | 112 | 91.8033 | |