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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
30051-30100 / 86044 show all | |||||||||||||||
| astatham-gatk | INDEL | D16_PLUS | map_siren | * | 93.3991 | 94.4056 | 92.4138 | 94.9653 | 135 | 8 | 134 | 11 | 2 | 18.1818 | |
| gduggal-snapplat | SNP | tv | map_l125_m2_e1 | * | 93.3986 | 91.2649 | 95.6344 | 83.1005 | 15202 | 1455 | 15203 | 694 | 360 | 51.8732 | |
| gduggal-snapfb | INDEL | D1_5 | map_l150_m0_e0 | het | 93.3985 | 94.5545 | 92.2705 | 87.9230 | 191 | 11 | 191 | 16 | 3 | 18.7500 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 93.3984 | 91.5194 | 95.3560 | 62.7021 | 259 | 24 | 308 | 15 | 12 | 80.0000 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.3973 | 93.3232 | 93.4716 | 64.9435 | 1230 | 88 | 1217 | 85 | 81 | 95.2941 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 93.3965 | 91.9097 | 94.9321 | 59.4498 | 28867 | 2541 | 29709 | 1586 | 1202 | 75.7881 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 93.3965 | 91.9097 | 94.9321 | 59.4498 | 28867 | 2541 | 29709 | 1586 | 1202 | 75.7881 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 93.3962 | 88.3929 | 99.0000 | 68.8474 | 99 | 13 | 99 | 1 | 1 | 100.0000 | |
| ciseli-custom | SNP | * | map_siren | homalt | 93.3935 | 93.4404 | 93.3467 | 52.8475 | 51538 | 3618 | 51210 | 3650 | 2749 | 75.3151 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 93.3929 | 89.2473 | 97.9424 | 67.1177 | 166 | 20 | 238 | 5 | 4 | 80.0000 | |
| gduggal-snapvard | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 93.3922 | 97.0358 | 90.0123 | 67.8126 | 53982 | 1649 | 53380 | 5923 | 338 | 5.7066 | |
| raldana-dualsentieon | INDEL | I1_5 | map_l250_m2_e0 | * | 93.3921 | 93.8053 | 92.9825 | 95.4272 | 106 | 7 | 106 | 8 | 1 | 12.5000 | |
| ltrigg-rtg1 | INDEL | D1_5 | map_l250_m2_e0 | het | 93.3921 | 87.6033 | 100.0000 | 89.4839 | 106 | 15 | 108 | 0 | 0 | ||
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.3918 | 87.9802 | 99.5128 | 30.5121 | 1603 | 219 | 1634 | 8 | 8 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.3918 | 87.9802 | 99.5128 | 30.5121 | 1603 | 219 | 1634 | 8 | 8 | 100.0000 | |
| gduggal-snapfb | INDEL | * | map_l150_m1_e0 | * | 93.3899 | 92.3019 | 94.5038 | 89.1529 | 1235 | 103 | 1238 | 72 | 21 | 29.1667 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 93.3883 | 91.3830 | 95.4836 | 39.3587 | 8643 | 815 | 9408 | 445 | 428 | 96.1798 | |
| ckim-vqsr | INDEL | * | HG002compoundhet | het | 93.3882 | 98.2169 | 89.0120 | 79.6916 | 4021 | 73 | 3775 | 466 | 457 | 98.0687 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 93.3879 | 93.2203 | 93.5561 | 66.6135 | 330 | 24 | 392 | 27 | 6 | 22.2222 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 93.3805 | 89.3617 | 97.7778 | 82.0000 | 42 | 5 | 44 | 1 | 1 | 100.0000 | |
| ltrigg-rtg1 | INDEL | * | map_l150_m0_e0 | het | 93.3791 | 88.8563 | 98.3871 | 82.7873 | 303 | 38 | 305 | 5 | 0 | 0.0000 | |
| gduggal-snapvard | SNP | * | map_l100_m2_e1 | het | 93.3754 | 96.7973 | 90.1872 | 78.6618 | 45396 | 1502 | 44805 | 4875 | 376 | 7.7128 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 93.3753 | 98.5816 | 88.6914 | 66.8807 | 556 | 8 | 549 | 70 | 69 | 98.5714 | |
| jpowers-varprowl | INDEL | I1_5 | map_siren | het | 93.3720 | 94.3486 | 92.4154 | 83.6731 | 1586 | 95 | 1584 | 130 | 105 | 80.7692 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 93.3712 | 87.5666 | 100.0000 | 59.6774 | 1972 | 280 | 1975 | 0 | 0 | ||
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.3705 | 92.2714 | 94.4961 | 50.6515 | 2543 | 213 | 2541 | 148 | 144 | 97.2973 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 93.3698 | 88.6709 | 98.5945 | 70.7743 | 1401 | 179 | 1403 | 20 | 6 | 30.0000 | |
| ltrigg-rtg1 | INDEL | * | map_l250_m0_e0 | * | 93.3679 | 89.7436 | 97.2973 | 95.8843 | 70 | 8 | 72 | 2 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | * | map_l250_m0_e0 | * | 93.3679 | 89.7436 | 97.2973 | 95.4037 | 70 | 8 | 72 | 2 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 93.3647 | 97.9109 | 89.2219 | 85.2038 | 1781 | 38 | 1548 | 187 | 133 | 71.1230 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 93.3647 | 97.9109 | 89.2219 | 85.2038 | 1781 | 38 | 1548 | 187 | 133 | 71.1230 | |
| 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-snapplat | SNP | tv | map_l125_m2_e0 | * | 93.3644 | 91.2184 | 95.6138 | 83.0664 | 15041 | 1448 | 15041 | 690 | 359 | 52.0290 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 93.3628 | 100.0000 | 87.5519 | 69.2994 | 211 | 0 | 211 | 30 | 29 | 96.6667 | |
| ciseli-custom | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 93.3626 | 97.9878 | 89.1544 | 38.6200 | 7207 | 148 | 7201 | 876 | 61 | 6.9635 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 93.3619 | 94.7826 | 91.9831 | 63.8720 | 218 | 12 | 218 | 19 | 12 | 63.1579 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.3618 | 90.6883 | 96.1977 | 79.5490 | 224 | 23 | 253 | 10 | 6 | 60.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 93.3603 | 88.9474 | 98.2340 | 60.9483 | 338 | 42 | 445 | 8 | 8 | 100.0000 | |
| asubramanian-gatk | INDEL | D6_15 | map_l100_m2_e0 | * | 93.3594 | 90.5303 | 96.3710 | 89.2314 | 239 | 25 | 239 | 9 | 3 | 33.3333 | |
| rpoplin-dv42 | INDEL | * | HG002compoundhet | * | 93.3591 | 92.7336 | 93.9930 | 68.4001 | 27783 | 2177 | 27758 | 1774 | 1747 | 98.4780 | |
| gduggal-bwaplat | INDEL | I1_5 | segdup | het | 93.3578 | 88.8476 | 98.3505 | 97.1410 | 478 | 60 | 477 | 8 | 5 | 62.5000 | |
| gduggal-snapplat | SNP | * | map_l100_m0_e0 | homalt | 93.3571 | 87.6248 | 99.8920 | 65.0376 | 10182 | 1438 | 10176 | 11 | 11 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | HG002complexvar | hetalt | 93.3550 | 91.2142 | 95.5988 | 55.5303 | 924 | 89 | 934 | 43 | 43 | 100.0000 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.3549 | 93.6842 | 93.0279 | 84.8155 | 623 | 42 | 467 | 35 | 31 | 88.5714 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.3545 | 97.0864 | 89.8990 | 74.7771 | 933 | 28 | 890 | 100 | 90 | 90.0000 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 93.3542 | 87.6993 | 99.7886 | 34.9381 | 385 | 54 | 472 | 1 | 1 | 100.0000 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 93.3541 | 87.9896 | 99.4152 | 75.0910 | 337 | 46 | 340 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 93.3540 | 87.6993 | 99.7881 | 34.6260 | 385 | 54 | 471 | 1 | 1 | 100.0000 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 93.3540 | 87.6993 | 99.7881 | 34.6260 | 385 | 54 | 471 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 93.3530 | 87.5346 | 100.0000 | 58.9909 | 316 | 45 | 317 | 0 | 0 | ||