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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
33951-34000 / 86044 show all | |||||||||||||||
| jli-custom | INDEL | D1_5 | map_l125_m2_e1 | homalt | 99.3271 | 99.1935 | 99.4609 | 85.1719 | 369 | 3 | 369 | 2 | 2 | 100.0000 | |
| anovak-vg | INDEL | D1_5 | map_l100_m2_e1 | het | 83.2523 | 87.6183 | 79.3007 | 85.1706 | 1111 | 157 | 1134 | 296 | 94 | 31.7568 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 61.6145 | 48.5714 | 84.2342 | 85.1703 | 187 | 198 | 187 | 35 | 5 | 14.2857 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 100.0000 | 100.0000 | 100.0000 | 85.1695 | 35 | 0 | 35 | 0 | 0 | ||
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 100.0000 | 100.0000 | 100.0000 | 85.1695 | 35 | 0 | 35 | 0 | 0 | ||
| gduggal-snapvard | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 75.9223 | 95.2075 | 63.1339 | 85.1688 | 1927 | 97 | 1942 | 1134 | 22 | 1.9400 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 80.2676 | 68.5714 | 96.7742 | 85.1675 | 24 | 11 | 30 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | INDEL | I1_5 | map_l150_m2_e1 | homalt | 97.2840 | 96.5686 | 98.0100 | 85.1661 | 197 | 7 | 197 | 4 | 2 | 50.0000 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 70.6236 | 94.0299 | 56.5476 | 85.1656 | 189 | 12 | 190 | 146 | 135 | 92.4658 | |
| gduggal-snapfb | INDEL | D6_15 | map_l125_m0_e0 | het | 80.3709 | 68.9655 | 96.2963 | 85.1648 | 20 | 9 | 26 | 1 | 1 | 100.0000 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.3799 | 94.7426 | 98.0747 | 85.1647 | 865 | 48 | 866 | 17 | 10 | 58.8235 | |
| jli-custom | INDEL | * | map_l100_m0_e0 | het | 97.8452 | 97.8452 | 97.8452 | 85.1642 | 999 | 22 | 999 | 22 | 5 | 22.7273 | |
| gduggal-snapfb | INDEL | I1_5 | map_l125_m1_e0 | het | 95.1089 | 95.6790 | 94.5455 | 85.1619 | 465 | 21 | 468 | 27 | 3 | 11.1111 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 80.3984 | 90.7602 | 72.1601 | 85.1616 | 776 | 79 | 775 | 299 | 5 | 1.6722 | |
| raldana-dualsentieon | INDEL | * | map_l125_m1_e0 | het | 97.3655 | 96.7790 | 97.9592 | 85.1598 | 1292 | 43 | 1296 | 27 | 3 | 11.1111 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.6785 | 100.0000 | 99.3590 | 85.1570 | 155 | 0 | 155 | 1 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | * | map_l100_m1_e0 | * | 98.3343 | 98.6615 | 98.0094 | 85.1549 | 3538 | 48 | 3545 | 72 | 17 | 23.6111 | |
| anovak-vg | INDEL | C1_5 | HG002complexvar | homalt | 0.0000 | 0.0000 | 91.6667 | 85.1546 | 0 | 0 | 66 | 6 | 4 | 66.6667 | |
| raldana-dualsentieon | INDEL | * | map_l125_m2_e0 | homalt | 98.6859 | 98.4273 | 98.9460 | 85.1526 | 751 | 12 | 751 | 8 | 3 | 37.5000 | |
| bgallagher-sentieon | INDEL | I1_5 | map_l125_m0_e0 | homalt | 98.7013 | 100.0000 | 97.4359 | 85.1523 | 114 | 0 | 114 | 3 | 2 | 66.6667 | |
| eyeh-varpipe | INDEL | D1_5 | map_l100_m1_e0 | homalt | 97.4137 | 98.4797 | 96.3705 | 85.1515 | 583 | 9 | 770 | 29 | 24 | 82.7586 | |
| ckim-dragen | INDEL | D1_5 | map_l125_m1_e0 | homalt | 98.7005 | 97.9943 | 99.4169 | 85.1515 | 342 | 7 | 341 | 2 | 2 | 100.0000 | |
| hfeng-pmm1 | INDEL | * | map_l125_m1_e0 | * | 97.9886 | 97.0574 | 98.9377 | 85.1509 | 2045 | 62 | 2049 | 22 | 4 | 18.1818 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.7711 | 88.5057 | 97.4684 | 85.1504 | 77 | 10 | 77 | 2 | 2 | 100.0000 | |
| ckim-dragen | INDEL | I6_15 | map_siren | homalt | 97.8261 | 100.0000 | 95.7447 | 85.1501 | 90 | 0 | 90 | 4 | 3 | 75.0000 | |
| mlin-fermikit | INDEL | D6_15 | map_l125_m2_e1 | * | 75.8724 | 69.5312 | 83.4862 | 85.1499 | 89 | 39 | 91 | 18 | 12 | 66.6667 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 100.0000 | 100.0000 | 100.0000 | 85.1485 | 15 | 0 | 15 | 0 | 0 | ||
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 100.0000 | 100.0000 | 100.0000 | 85.1485 | 15 | 0 | 15 | 0 | 0 | ||
| raldana-dualsentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 100.0000 | 100.0000 | 100.0000 | 85.1485 | 15 | 0 | 15 | 0 | 0 | ||
| raldana-dualsentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 100.0000 | 100.0000 | 100.0000 | 85.1485 | 15 | 0 | 15 | 0 | 0 | ||
| dgrover-gatk | INDEL | I1_5 | map_l100_m2_e0 | * | 98.9764 | 98.8304 | 99.1228 | 85.1466 | 1352 | 16 | 1356 | 12 | 4 | 33.3333 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 87.7327 | 97.7687 | 79.5653 | 85.1430 | 10560 | 241 | 10653 | 2736 | 243 | 8.8816 | |
| gduggal-bwafb | INDEL | * | map_l100_m0_e0 | * | 96.4693 | 95.1376 | 97.8389 | 85.1430 | 1487 | 76 | 1494 | 33 | 7 | 21.2121 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 99.3133 | 98.8433 | 99.7877 | 85.1420 | 940 | 11 | 940 | 2 | 2 | 100.0000 | |
| jpowers-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 90.7947 | 97.9343 | 84.6254 | 85.1417 | 14270 | 301 | 14322 | 2602 | 202 | 7.7633 | |
| jpowers-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 90.7947 | 97.9343 | 84.6254 | 85.1417 | 14270 | 301 | 14322 | 2602 | 202 | 7.7633 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.4939 | 96.6013 | 98.4032 | 85.1394 | 1478 | 52 | 1479 | 24 | 16 | 66.6667 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.4939 | 96.6013 | 98.4032 | 85.1394 | 1478 | 52 | 1479 | 24 | 16 | 66.6667 | |
| mlin-fermikit | INDEL | * | map_l150_m2_e1 | * | 65.1571 | 52.8145 | 85.0279 | 85.1378 | 760 | 679 | 761 | 134 | 106 | 79.1045 | |
| gduggal-bwaplat | SNP | ti | map_l150_m2_e0 | homalt | 60.4067 | 43.2904 | 99.9090 | 85.1344 | 3297 | 4319 | 3293 | 3 | 3 | 100.0000 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 61.4131 | 61.8391 | 60.9929 | 85.1344 | 269 | 166 | 344 | 220 | 13 | 5.9091 | |
| ltrigg-rtg1 | INDEL | * | map_l125_m2_e1 | homalt | 99.0968 | 99.0956 | 99.0979 | 85.1341 | 767 | 7 | 769 | 7 | 3 | 42.8571 | |
| ckim-isaac | SNP | ti | map_l250_m2_e0 | homalt | 62.2886 | 45.2830 | 99.7481 | 85.1339 | 792 | 957 | 792 | 2 | 2 | 100.0000 | |
| jli-custom | INDEL | D1_5 | map_l125_m1_e0 | het | 98.4902 | 98.7603 | 98.2216 | 85.1332 | 717 | 9 | 718 | 13 | 3 | 23.0769 | |
| raldana-dualsentieon | INDEL | D1_5 | map_l125_m2_e1 | het | 97.9827 | 97.6623 | 98.3051 | 85.1328 | 752 | 18 | 754 | 13 | 2 | 15.3846 | |
| eyeh-varpipe | INDEL | I1_5 | map_l125_m2_e1 | homalt | 98.6596 | 99.1254 | 98.1982 | 85.1326 | 340 | 3 | 545 | 10 | 9 | 90.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | map_l100_m0_e0 | het | 98.2965 | 97.2393 | 99.3769 | 85.1320 | 317 | 9 | 319 | 2 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | D1_5 | map_l100_m0_e0 | * | 97.6164 | 97.3349 | 97.8996 | 85.1319 | 840 | 23 | 839 | 18 | 1 | 5.5556 | |
| ckim-dragen | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.7368 | 98.6330 | 98.8409 | 85.1301 | 938 | 13 | 938 | 11 | 4 | 36.3636 | |
| ltrigg-rtg1 | INDEL | * | map_l125_m2_e0 | homalt | 99.2113 | 99.0826 | 99.3404 | 85.1285 | 756 | 7 | 753 | 5 | 3 | 60.0000 | |