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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
5151-5200 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.1341 | 96.7259 | 99.5838 | 73.0521 | 15067 | 510 | 15075 | 63 | 45 | 71.4286 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.7812 | 96.5482 | 99.0462 | 60.2645 | 15216 | 544 | 15057 | 145 | 123 | 84.8276 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.7589 | 96.5419 | 99.0070 | 60.1541 | 15215 | 545 | 15055 | 151 | 115 | 76.1589 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.7933 | 96.5102 | 99.1110 | 60.0852 | 15210 | 550 | 15051 | 135 | 117 | 86.6667 | |
| ckim-vqsr | SNP | * | map_l150_m1_e0 | * | 65.6433 | 49.1783 | 98.6821 | 91.1099 | 15053 | 15556 | 15050 | 201 | 2 | 0.9950 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.9259 | 94.5255 | 99.4514 | 70.4506 | 14573 | 844 | 15046 | 83 | 82 | 98.7952 | |
| gduggal-snapplat | SNP | tv | map_l125_m2_e0 | * | 93.3644 | 91.2184 | 95.6138 | 83.0664 | 15041 | 1448 | 15041 | 690 | 359 | 52.0290 | |
| gduggal-snapplat | SNP | * | map_l125_m1_e0 | homalt | 94.1655 | 89.0269 | 99.9336 | 67.4179 | 15050 | 1855 | 15040 | 10 | 9 | 90.0000 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.6431 | 96.1084 | 99.2277 | 42.1750 | 10002 | 405 | 15032 | 117 | 72 | 61.5385 | |
| raldana-dualsentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.3115 | 96.3071 | 98.3370 | 59.4348 | 15178 | 582 | 15020 | 254 | 229 | 90.1575 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 48.9009 | 46.9867 | 50.9776 | 50.1691 | 15032 | 16960 | 15018 | 14442 | 14205 | 98.3590 | |
| ciseli-custom | SNP | * | map_l125_m2_e0 | homalt | 88.1697 | 86.6763 | 89.7155 | 68.5746 | 15060 | 2315 | 15013 | 1721 | 1379 | 80.1278 | |
| asubramanian-gatk | SNP | ti | map_l100_m2_e1 | het | 65.2727 | 48.4981 | 99.7873 | 85.9875 | 15015 | 15945 | 15011 | 32 | 12 | 37.5000 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.4030 | 99.1198 | 99.6877 | 55.5385 | 14640 | 130 | 15005 | 47 | 23 | 48.9362 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.4540 | 96.3472 | 98.5866 | 68.3439 | 15008 | 569 | 14997 | 215 | 126 | 58.6047 | |
| mlin-fermikit | SNP | tv | map_l100_m2_e1 | * | 71.2430 | 59.3165 | 89.1725 | 57.7345 | 14997 | 10286 | 14989 | 1820 | 1600 | 87.9121 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 84.4168 | 96.1004 | 75.2662 | 52.8425 | 14047 | 570 | 14984 | 4924 | 4785 | 97.1771 | |
| jpowers-varprowl | SNP | tv | map_l100_m1_e0 | het | 96.9444 | 97.1330 | 96.7565 | 74.5209 | 14975 | 442 | 14975 | 502 | 99 | 19.7211 | |
| gduggal-snapvard | SNP | tv | map_l100_m1_e0 | het | 92.4877 | 97.3990 | 88.0480 | 78.4967 | 15016 | 401 | 14962 | 2031 | 139 | 6.8439 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 57.8916 | 83.4278 | 44.3245 | 56.1428 | 14866 | 2953 | 14940 | 18766 | 18665 | 99.4618 | |
| dgrover-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.8320 | 96.0887 | 99.6397 | 60.4528 | 14814 | 603 | 14932 | 54 | 53 | 98.1481 | |
| gduggal-snapplat | SNP | tv | map_l100_m2_e0 | het | 94.7121 | 94.6314 | 94.7930 | 82.9183 | 14930 | 847 | 14928 | 820 | 395 | 48.1707 | |
| ciseli-custom | SNP | ti | HG002compoundhet | * | 76.3715 | 85.1127 | 69.2586 | 41.8951 | 14876 | 2602 | 14928 | 6626 | 715 | 10.7908 | |
| astatham-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.7545 | 95.9460 | 99.6325 | 60.1730 | 14792 | 625 | 14910 | 55 | 54 | 98.1818 | |
| hfeng-pmm1 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.9045 | 95.9136 | 99.9799 | 60.6514 | 14787 | 630 | 14905 | 3 | 2 | 66.6667 | |
| asubramanian-gatk | SNP | * | map_l125_m2_e1 | * | 47.9740 | 31.5792 | 99.7724 | 91.5607 | 14906 | 32296 | 14903 | 34 | 8 | 23.5294 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 95.1482 | 96.8620 | 93.4939 | 39.6090 | 10032 | 325 | 14902 | 1037 | 946 | 91.2247 | |
| hfeng-pmm2 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.8168 | 95.7514 | 99.9731 | 60.5697 | 14762 | 655 | 14877 | 4 | 3 | 75.0000 | |
| ckim-gatk | SNP | ti | map_l125_m1_e0 | het | 88.7011 | 81.4464 | 97.3746 | 85.8996 | 14877 | 3389 | 14873 | 401 | 40 | 9.9751 | |
| ckim-isaac | SNP | tv | map_l100_m1_e0 | * | 75.3790 | 60.5730 | 99.7648 | 65.1235 | 14841 | 9660 | 14844 | 35 | 12 | 34.2857 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 41.5565 | 39.2117 | 44.1996 | 50.5594 | 14862 | 23040 | 14844 | 18740 | 18573 | 99.1089 | |
| jmaeng-gatk | SNP | ti | map_l125_m1_e0 | het | 88.5520 | 81.2876 | 97.2421 | 86.2223 | 14848 | 3418 | 14844 | 421 | 39 | 9.2637 | |
| hfeng-pmm3 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.6708 | 95.4660 | 99.9798 | 58.6016 | 14718 | 699 | 14835 | 3 | 2 | 66.6667 | |
| mlin-fermikit | SNP | tv | map_l100_m2_e0 | * | 71.0756 | 59.1180 | 89.0970 | 57.6083 | 14799 | 10234 | 14791 | 1810 | 1594 | 88.0663 | |
| asubramanian-gatk | SNP | ti | map_l100_m2_e0 | het | 65.0317 | 48.2333 | 99.7838 | 86.0511 | 14770 | 15852 | 14766 | 32 | 12 | 37.5000 | |
| ckim-dragen | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.2357 | 94.9731 | 99.6087 | 58.9389 | 14642 | 775 | 14763 | 58 | 58 | 100.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.2548 | 94.9731 | 99.6489 | 58.8526 | 14642 | 775 | 14759 | 52 | 52 | 100.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8950 | 99.8510 | 99.9390 | 54.8240 | 14748 | 22 | 14750 | 9 | 4 | 44.4444 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8578 | 99.8307 | 99.8849 | 56.2250 | 14745 | 25 | 14747 | 17 | 4 | 23.5294 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8747 | 99.8104 | 99.9390 | 55.0186 | 14742 | 28 | 14744 | 9 | 4 | 44.4444 | |
| jli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8713 | 99.8037 | 99.9390 | 54.3200 | 14741 | 29 | 14742 | 9 | 4 | 44.4444 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8273 | 99.7901 | 99.8645 | 55.6157 | 14739 | 31 | 14740 | 20 | 5 | 25.0000 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 64.5823 | 60.5420 | 69.2004 | 40.5056 | 14857 | 9683 | 14739 | 6560 | 6397 | 97.5152 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7395 | 99.7766 | 99.7024 | 56.2348 | 14737 | 33 | 14739 | 44 | 17 | 38.6364 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7968 | 99.7563 | 99.8374 | 54.8306 | 14734 | 36 | 14736 | 24 | 17 | 70.8333 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.1334 | 94.7850 | 99.6011 | 59.6178 | 14613 | 804 | 14733 | 59 | 58 | 98.3051 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8103 | 99.7360 | 99.8847 | 56.3092 | 14731 | 39 | 14733 | 17 | 4 | 23.5294 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 47.3491 | 46.0834 | 48.6863 | 59.5527 | 14743 | 17249 | 14732 | 15527 | 15257 | 98.2611 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8000 | 99.6479 | 99.9525 | 54.9426 | 14718 | 52 | 14720 | 7 | 1 | 14.2857 | |
| anovak-vg | SNP | tv | map_l100_m2_e1 | het | 80.1681 | 92.4332 | 70.7766 | 74.1911 | 14732 | 1206 | 14718 | 6077 | 1278 | 21.0301 | |