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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
65151-65200 / 86044 show all | |||||||||||||||
| cchapple-custom | SNP | ti | func_cds | * | 99.8586 | 99.9202 | 99.7971 | 24.6780 | 13776 | 11 | 13774 | 28 | 1 | 3.5714 | |
| gduggal-bwavard | SNP | ti | * | het | 99.2556 | 99.0550 | 99.4571 | 24.6552 | 1269783 | 12114 | 1265789 | 6910 | 2002 | 28.9725 | |
| dgrover-gatk | INDEL | D6_15 | HG002compoundhet | hetalt | 97.2251 | 94.9945 | 99.5630 | 24.6392 | 7743 | 408 | 7747 | 34 | 33 | 97.0588 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 98.0000 | 96.0784 | 100.0000 | 24.6377 | 49 | 2 | 52 | 0 | 0 | ||
| dgrover-gatk | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 24.6351 | 1704 | 0 | 1704 | 0 | 0 | ||
| astatham-gatk | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 24.6351 | 1704 | 0 | 1704 | 0 | 0 | ||
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.6894 | 93.8694 | 99.6841 | 24.6230 | 3782 | 247 | 3787 | 12 | 12 | 100.0000 | |
| jli-custom | INDEL | D16_PLUS | HG002compoundhet | hetalt | 97.5241 | 95.5394 | 99.5931 | 24.6166 | 1842 | 86 | 1958 | 8 | 8 | 100.0000 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 84.2593 | 72.8000 | 100.0000 | 24.6032 | 91 | 34 | 95 | 0 | 0 | ||
| bgallagher-sentieon | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 24.6018 | 1704 | 0 | 1704 | 0 | 0 | ||
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.3148 | 95.2850 | 99.4329 | 24.6012 | 4547 | 225 | 4559 | 26 | 26 | 100.0000 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 95.4396 | 91.6508 | 99.5551 | 24.5986 | 6257 | 570 | 6265 | 28 | 25 | 89.2857 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 96.8421 | 93.8776 | 100.0000 | 24.5902 | 46 | 3 | 46 | 0 | 0 | ||
| gduggal-bwaplat | SNP | tv | HG002complexvar | homalt | 97.7875 | 95.7534 | 99.9100 | 24.5806 | 91072 | 4039 | 90999 | 82 | 77 | 93.9024 | |
| ckim-isaac | INDEL | D16_PLUS | HG002compoundhet | hetalt | 86.1574 | 76.3485 | 98.8582 | 24.5694 | 1472 | 456 | 1645 | 19 | 17 | 89.4737 | |
| anovak-vg | SNP | tv | * | * | 98.3366 | 98.3717 | 98.3016 | 24.5602 | 953908 | 15790 | 951566 | 16441 | 6526 | 39.6934 | |
| ckim-dragen | SNP | * | * | het | 99.7355 | 99.9519 | 99.5199 | 24.5349 | 1872686 | 901 | 1873038 | 9035 | 444 | 4.9142 | |
| mlin-fermikit | INDEL | I1_5 | func_cds | homalt | 99.5816 | 100.0000 | 99.1667 | 24.5283 | 119 | 0 | 119 | 1 | 1 | 100.0000 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.7679 | 94.4049 | 99.2523 | 24.5186 | 4505 | 267 | 4513 | 34 | 33 | 97.0588 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 51.6683 | 38.0989 | 80.2508 | 24.4970 | 501 | 814 | 512 | 126 | 126 | 100.0000 | |
| mlin-fermikit | SNP | tv | HG002complexvar | homalt | 98.2029 | 98.2799 | 98.1261 | 24.4893 | 93475 | 1636 | 93471 | 1785 | 1729 | 96.8627 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.4580 | 95.5784 | 99.4130 | 24.4663 | 4561 | 211 | 4573 | 27 | 27 | 100.0000 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.4690 | 95.5993 | 99.4132 | 24.4623 | 4562 | 210 | 4574 | 27 | 27 | 100.0000 | |
| astatham-gatk | INDEL | D6_15 | HG002compoundhet | hetalt | 97.1670 | 94.8841 | 99.5625 | 24.4483 | 7734 | 417 | 7738 | 34 | 33 | 97.0588 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.1124 | 95.2081 | 99.0944 | 24.4379 | 755 | 38 | 766 | 7 | 6 | 85.7143 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.7006 | 96.2169 | 99.2308 | 24.4186 | 763 | 30 | 774 | 6 | 6 | 100.0000 | |
| ghariani-varprowl | INDEL | D1_5 | func_cds | homalt | 92.0863 | 86.4865 | 98.4615 | 24.4186 | 64 | 10 | 64 | 1 | 0 | 0.0000 | |
| jpowers-varprowl | SNP | tv | HG002complexvar | * | 99.3235 | 99.1623 | 99.4852 | 24.4097 | 244090 | 2062 | 244285 | 1264 | 803 | 63.5285 | |
| gduggal-snapplat | SNP | ti | * | * | 99.1814 | 98.9158 | 99.4485 | 24.4080 | 2062907 | 22611 | 2063333 | 11443 | 1808 | 15.8001 | |
| ciseli-custom | SNP | tv | HG002complexvar | * | 94.9824 | 96.7736 | 93.2564 | 24.4003 | 238213 | 7942 | 236085 | 17072 | 2875 | 16.8404 | |
| hfeng-pmm3 | SNP | * | func_cds | het | 99.9015 | 99.9552 | 99.8478 | 24.3993 | 11156 | 5 | 11153 | 17 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 97.8947 | 95.8763 | 100.0000 | 24.3902 | 93 | 4 | 93 | 0 | 0 | ||
| gduggal-snapfb | SNP | * | func_cds | homalt | 99.9570 | 99.9857 | 99.9284 | 24.3691 | 6978 | 1 | 6978 | 5 | 1 | 20.0000 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 96.5279 | 94.3253 | 98.8357 | 24.3640 | 748 | 45 | 764 | 9 | 8 | 88.8889 | |
| jlack-gatk | INDEL | D6_15 | HG002compoundhet | hetalt | 94.7748 | 90.4552 | 99.5278 | 24.3596 | 7373 | 778 | 7377 | 35 | 30 | 85.7143 | |
| cchapple-custom | INDEL | I1_5 | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 24.3590 | 119 | 0 | 118 | 0 | 0 | ||
| asubramanian-gatk | SNP | tv | * | * | 98.7904 | 97.7276 | 99.8765 | 24.3508 | 947655 | 22035 | 947577 | 1172 | 61 | 5.2048 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 63.5773 | 97.5422 | 47.1569 | 24.3464 | 1905 | 48 | 1924 | 2156 | 2141 | 99.3043 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.6223 | 93.7986 | 99.6213 | 24.3454 | 7593 | 502 | 7628 | 29 | 29 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.6289 | 93.8110 | 99.6213 | 24.3430 | 7594 | 501 | 7629 | 29 | 29 | 100.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | HG002compoundhet | hetalt | 90.6567 | 83.2469 | 99.5146 | 24.3343 | 1605 | 323 | 1640 | 8 | 8 | 100.0000 | |
| anovak-vg | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 97.9888 | 97.4071 | 98.5775 | 24.3272 | 1390 | 37 | 1386 | 20 | 20 | 100.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.3002 | 94.7561 | 99.9846 | 24.3136 | 6469 | 358 | 6477 | 1 | 0 | 0.0000 | |
| raldana-dualsentieon | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 24.3003 | 1704 | 0 | 1704 | 0 | 0 | ||
| ckim-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 76.3320 | 62.0112 | 99.2537 | 24.2938 | 111 | 68 | 133 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 76.3320 | 62.0112 | 99.2537 | 24.2938 | 111 | 68 | 133 | 1 | 1 | 100.0000 | |
| gduggal-snapvard | INDEL | * | func_cds | homalt | 88.1855 | 79.2035 | 99.4652 | 24.2915 | 179 | 47 | 186 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.0099 | 98.0392 | 100.0000 | 24.2857 | 50 | 1 | 53 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.7886 | 99.5781 | 100.0000 | 24.2812 | 236 | 1 | 237 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.9389 | 94.3899 | 99.6295 | 24.2810 | 6444 | 383 | 6453 | 24 | 24 | 100.0000 | |