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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
83251-83300 / 86044 show all | |||||||||||||||
| gduggal-snapfb | SNP | ti | map_l100_m2_e0 | * | 97.7846 | 97.7165 | 97.8527 | 68.4501 | 47843 | 1118 | 47848 | 1050 | 457 | 43.5238 | |
| gduggal-snapfb | SNP | ti | map_l100_m2_e1 | * | 97.8010 | 97.7367 | 97.8655 | 68.4763 | 48365 | 1120 | 48370 | 1055 | 457 | 43.3175 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.8573 | 92.4054 | 93.3136 | 74.7428 | 9308 | 765 | 9462 | 678 | 457 | 67.4041 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 56.1615 | 41.5637 | 86.5642 | 60.9124 | 3397 | 4776 | 3434 | 533 | 458 | 85.9287 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 60.5053 | 81.8731 | 47.9826 | 72.9778 | 542 | 120 | 880 | 954 | 458 | 48.0084 | |
| gduggal-snapplat | INDEL | * | HG002complexvar | het | 73.0648 | 65.5393 | 82.5428 | 64.5149 | 30287 | 15925 | 32942 | 6967 | 459 | 6.5882 | |
| dgrover-gatk | INDEL | * | HG002compoundhet | het | 93.5069 | 98.4612 | 89.0273 | 79.7555 | 4031 | 63 | 3789 | 467 | 459 | 98.2869 | |
| jpowers-varprowl | SNP | * | * | het | 99.3161 | 99.3290 | 99.3033 | 25.1238 | 1861010 | 12572 | 1861335 | 13059 | 459 | 3.5148 | |
| ciseli-custom | SNP | * | map_l150_m0_e0 | homalt | 84.0715 | 82.7097 | 85.4790 | 75.1182 | 3382 | 707 | 3373 | 573 | 459 | 80.1047 | |
| asubramanian-gatk | INDEL | * | HG002compoundhet | het | 90.4926 | 96.2872 | 85.3557 | 79.1653 | 3942 | 152 | 3707 | 636 | 459 | 72.1698 | |
| mlin-fermikit | SNP | ti | map_l150_m0_e0 | homalt | 53.2251 | 42.7381 | 70.5320 | 59.3142 | 1180 | 1581 | 1180 | 493 | 459 | 93.1034 | |
| qzeng-custom | SNP | * | map_l125_m0_e0 | het | 78.6100 | 67.5932 | 93.9173 | 91.2651 | 8560 | 4104 | 8492 | 550 | 460 | 83.6364 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 24.6578 | 16.3033 | 50.5747 | 64.7773 | 486 | 2495 | 484 | 473 | 460 | 97.2516 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 26.7835 | 20.7451 | 37.7805 | 22.4371 | 245 | 936 | 303 | 499 | 460 | 92.1844 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 45.0912 | 56.0811 | 37.7029 | 22.3084 | 83 | 65 | 302 | 499 | 460 | 92.1844 | |
| gduggal-snapplat | SNP | ti | map_l150_m2_e0 | het | 93.1053 | 92.6481 | 93.5671 | 87.2010 | 11934 | 947 | 11956 | 822 | 460 | 55.9611 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 79.0223 | 86.0771 | 73.0363 | 71.1846 | 915 | 148 | 1590 | 587 | 460 | 78.3646 | |
| jlack-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.1165 | 99.7497 | 98.4914 | 72.1867 | 30684 | 77 | 30684 | 470 | 460 | 97.8723 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 48.6065 | 77.8364 | 35.3365 | 53.6490 | 295 | 84 | 294 | 538 | 460 | 85.5019 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 80.7660 | 81.6777 | 79.8745 | 42.7070 | 3330 | 747 | 3310 | 834 | 461 | 55.2758 | |
| ciseli-custom | SNP | tv | map_l125_m1_e0 | homalt | 87.0129 | 84.8123 | 89.3307 | 67.3979 | 4970 | 890 | 4965 | 593 | 461 | 77.7403 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 97.1997 | 99.7848 | 94.7452 | 59.6307 | 8348 | 18 | 8348 | 463 | 461 | 99.5680 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.4986 | 96.2849 | 98.7434 | 52.0928 | 17157 | 662 | 43140 | 549 | 461 | 83.9709 | |
| cchapple-custom | INDEL | * | HG002complexvar | * | 98.8567 | 98.4455 | 99.2713 | 55.5354 | 75742 | 1196 | 78742 | 578 | 462 | 79.9308 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 49.8749 | 48.6428 | 51.1711 | 72.7940 | 896 | 946 | 1005 | 959 | 462 | 48.1752 | |
| mlin-fermikit | SNP | ti | map_l150_m0_e0 | * | 48.0167 | 33.6471 | 83.8086 | 63.2254 | 2645 | 5216 | 2645 | 511 | 462 | 90.4110 | |
| ckim-isaac | SNP | ti | * | * | 98.6272 | 97.3318 | 99.9576 | 14.8667 | 2029873 | 55645 | 2030218 | 862 | 462 | 53.5963 | |
| ciseli-custom | INDEL | I16_PLUS | HG002compoundhet | * | 0.6022 | 0.3733 | 1.5564 | 60.4311 | 8 | 2135 | 8 | 506 | 462 | 91.3043 | |
| gduggal-snapplat | SNP | ti | map_l150_m2_e1 | het | 93.1452 | 92.6854 | 93.6096 | 87.2522 | 12063 | 952 | 12085 | 825 | 463 | 56.1212 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 95.1935 | 94.2916 | 96.1127 | 68.3224 | 16006 | 969 | 16096 | 651 | 464 | 71.2750 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.1935 | 94.2916 | 96.1127 | 68.3224 | 16006 | 969 | 16096 | 651 | 464 | 71.2750 | |
| gduggal-bwafb | SNP | * | HG002complexvar | * | 99.8109 | 99.7664 | 99.8554 | 20.0831 | 752623 | 1762 | 752783 | 1090 | 464 | 42.5688 | |
| ckim-gatk | INDEL | * | HG002compoundhet | het | 93.4586 | 98.5589 | 88.8602 | 79.6039 | 4035 | 59 | 3789 | 475 | 465 | 97.8947 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.4911 | 99.7899 | 95.2959 | 55.3475 | 9501 | 20 | 9501 | 469 | 465 | 99.1471 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.8737 | 96.6718 | 99.1058 | 64.7457 | 63176 | 2175 | 62956 | 568 | 465 | 81.8662 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.8737 | 96.6718 | 99.1058 | 64.7457 | 63176 | 2175 | 62956 | 568 | 465 | 81.8662 | |
| bgallagher-sentieon | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.1594 | 93.5769 | 94.7492 | 68.8883 | 9426 | 647 | 9275 | 514 | 466 | 90.6615 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 59.1118 | 53.1250 | 66.6194 | 50.7504 | 952 | 840 | 940 | 471 | 467 | 99.1507 | |
| gduggal-snapplat | SNP | ti | map_l100_m0_e0 | het | 93.3645 | 92.7197 | 94.0184 | 82.6234 | 12965 | 1018 | 12983 | 826 | 467 | 56.5375 | |
| gduggal-snapfb | INDEL | I1_5 | HG002complexvar | het | 93.2070 | 95.4203 | 91.0940 | 55.8992 | 17356 | 833 | 18135 | 1773 | 467 | 26.3395 | |
| ndellapenna-hhga | SNP | * | * | * | 99.8818 | 99.8118 | 99.9519 | 18.1821 | 3048871 | 5748 | 3048919 | 1468 | 467 | 31.8120 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 76.7383 | 75.0311 | 78.5249 | 51.9191 | 1809 | 602 | 1810 | 495 | 467 | 94.3434 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 90.3594 | 91.9064 | 88.8636 | 53.3705 | 5144 | 453 | 4684 | 587 | 468 | 79.7274 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9638 | 97.4619 | 98.4709 | 54.8834 | 31180 | 812 | 31104 | 483 | 468 | 96.8944 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.2893 | 95.0573 | 97.5536 | 44.7868 | 19578 | 1018 | 19579 | 491 | 468 | 95.3157 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.0520 | 97.3439 | 98.7704 | 57.5661 | 42184 | 1151 | 42011 | 523 | 468 | 89.4837 | |
| gduggal-snapplat | SNP | ti | map_l150_m1_e0 | * | 92.9132 | 90.4018 | 95.5681 | 83.3799 | 17820 | 1892 | 17833 | 827 | 469 | 56.7110 | |
| anovak-vg | INDEL | I1_5 | map_l100_m2_e1 | * | 57.8586 | 58.9964 | 56.7639 | 84.9109 | 823 | 572 | 856 | 652 | 469 | 71.9325 | |
| anovak-vg | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.4699 | 97.9603 | 96.9843 | 55.7493 | 19787 | 412 | 20132 | 626 | 469 | 74.9201 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 89.7118 | 87.9829 | 91.5099 | 73.1427 | 5352 | 731 | 5303 | 492 | 469 | 95.3252 | |