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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
7701-7750 / 86044 show all | |||||||||||||||
| ckim-dragen | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.2779 | 95.1269 | 99.5285 | 62.9323 | 8843 | 453 | 8865 | 42 | 42 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 93.3264 | 87.6955 | 99.7299 | 56.2023 | 8859 | 1243 | 8863 | 24 | 19 | 79.1667 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.1571 | 94.8660 | 99.5615 | 32.7282 | 8814 | 477 | 8855 | 39 | 37 | 94.8718 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.1571 | 94.8660 | 99.5615 | 32.7282 | 8814 | 477 | 8855 | 39 | 37 | 94.8718 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.2540 | 95.0409 | 99.5726 | 63.0163 | 8835 | 461 | 8854 | 38 | 38 | 100.0000 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.4574 | 95.0409 | 100.0000 | 63.3890 | 8835 | 461 | 8854 | 0 | 0 | ||
| asubramanian-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.9370 | 94.9441 | 99.0153 | 65.4795 | 8826 | 470 | 8849 | 88 | 83 | 94.3182 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.0603 | 94.6723 | 99.5719 | 32.5070 | 8796 | 495 | 8838 | 38 | 37 | 97.3684 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.0603 | 94.6723 | 99.5719 | 32.5070 | 8796 | 495 | 8838 | 38 | 37 | 97.3684 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.1124 | 94.7719 | 99.5714 | 64.0050 | 8810 | 486 | 8829 | 38 | 38 | 100.0000 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 78.4631 | 67.4647 | 93.7460 | 41.7311 | 3776 | 1821 | 8829 | 589 | 574 | 97.4533 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.1068 | 94.7612 | 99.5714 | 64.0076 | 8809 | 487 | 8828 | 38 | 38 | 100.0000 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 77.1546 | 63.0485 | 99.3919 | 33.0569 | 8678 | 5086 | 8826 | 54 | 53 | 98.1481 | |
| ckim-isaac | SNP | * | map_l125_m2_e0 | homalt | 67.3485 | 50.7856 | 99.9434 | 65.6165 | 8824 | 8551 | 8824 | 5 | 5 | 100.0000 | |
| ckim-gatk | SNP | tv | HG002compoundhet | * | 99.2966 | 98.8905 | 99.7061 | 49.4688 | 8824 | 99 | 8821 | 26 | 17 | 65.3846 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.6948 | 94.0803 | 99.4587 | 42.1375 | 8741 | 550 | 8820 | 48 | 47 | 97.9167 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.6948 | 94.0803 | 99.4587 | 42.1375 | 8741 | 550 | 8820 | 48 | 47 | 97.9167 | |
| asubramanian-gatk | SNP | tv | map_siren | homalt | 67.6949 | 51.1717 | 99.9773 | 68.4987 | 8822 | 8418 | 8819 | 2 | 2 | 100.0000 | |
| cchapple-custom | SNP | tv | map_l100_m1_e0 | homalt | 98.7629 | 97.5561 | 100.0000 | 57.4941 | 8822 | 221 | 8817 | 0 | 0 | ||
| gduggal-snapfb | SNP | tv | HG002compoundhet | * | 79.6649 | 97.8931 | 67.1595 | 54.5136 | 8735 | 188 | 8812 | 4309 | 247 | 5.7322 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.0103 | 94.5783 | 99.5706 | 64.1494 | 8792 | 504 | 8811 | 38 | 38 | 100.0000 | |
| jmaeng-gatk | SNP | tv | HG002compoundhet | * | 99.2678 | 98.7672 | 99.7735 | 49.6292 | 8813 | 110 | 8810 | 20 | 17 | 85.0000 | |
| gduggal-bwaplat | SNP | ti | map_l100_m0_e0 | het | 76.9732 | 62.9193 | 99.1113 | 88.0688 | 8798 | 5185 | 8810 | 79 | 24 | 30.3797 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 76.4899 | 74.2821 | 78.8329 | 50.1539 | 8821 | 3054 | 8808 | 2365 | 2266 | 95.8140 | |
| gduggal-bwavard | SNP | tv | map_l100_m1_e0 | homalt | 98.7927 | 97.7441 | 99.8639 | 61.4588 | 8839 | 204 | 8807 | 12 | 10 | 83.3333 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 66.2291 | 94.8867 | 50.8665 | 79.7967 | 8666 | 467 | 8806 | 8506 | 164 | 1.9281 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 66.2291 | 94.8867 | 50.8665 | 79.7967 | 8666 | 467 | 8806 | 8506 | 164 | 1.9281 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.0416 | 94.2633 | 99.9886 | 32.8733 | 8758 | 533 | 8802 | 1 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.0416 | 94.2633 | 99.9886 | 32.8733 | 8758 | 533 | 8802 | 1 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | D6_15 | HG002compoundhet | * | 88.7012 | 84.9518 | 92.7969 | 32.0774 | 7672 | 1359 | 8799 | 683 | 663 | 97.0717 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 92.7405 | 88.7846 | 97.0653 | 58.2458 | 8605 | 1087 | 8798 | 266 | 144 | 54.1353 | |
| gduggal-snapfb | SNP | tv | map_l100_m1_e0 | homalt | 98.3618 | 97.2686 | 99.4798 | 71.8035 | 8796 | 247 | 8797 | 46 | 9 | 19.5652 | |
| ltrigg-rtg2 | SNP | tv | HG002compoundhet | * | 99.3414 | 98.9802 | 99.7052 | 44.7928 | 8832 | 91 | 8795 | 26 | 6 | 23.0769 | |
| astatham-gatk | SNP | tv | HG002compoundhet | * | 99.1767 | 98.5543 | 99.8069 | 49.0836 | 8794 | 129 | 8789 | 17 | 16 | 94.1176 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.9506 | 94.1018 | 99.9772 | 33.0820 | 8743 | 548 | 8785 | 2 | 1 | 50.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.9506 | 94.1018 | 99.9772 | 33.0820 | 8743 | 548 | 8785 | 2 | 1 | 50.0000 | |
| anovak-vg | SNP | * | map_l150_m1_e0 | homalt | 87.8735 | 78.8344 | 99.2540 | 70.4677 | 8887 | 2386 | 8781 | 66 | 54 | 81.8182 | |
| gduggal-bwaplat | INDEL | I1_5 | HG002compoundhet | * | 82.1492 | 71.0667 | 97.3270 | 74.9005 | 8781 | 3575 | 8775 | 241 | 126 | 52.2822 | |
| mlin-fermikit | SNP | tv | map_l100_m2_e1 | het | 70.6499 | 55.0822 | 98.4842 | 60.7475 | 8779 | 7159 | 8771 | 135 | 2 | 1.4815 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 63.8421 | 54.7304 | 76.5939 | 75.6642 | 8799 | 7278 | 8770 | 2680 | 2299 | 85.7836 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 63.8421 | 54.7304 | 76.5939 | 75.6642 | 8799 | 7278 | 8770 | 2680 | 2299 | 85.7836 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.6722 | 93.9296 | 99.5798 | 30.8791 | 8727 | 564 | 8769 | 37 | 37 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.6722 | 93.9296 | 99.5798 | 30.8791 | 8727 | 564 | 8769 | 37 | 37 | 100.0000 | |
| gduggal-bwafb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 93.6596 | 95.7079 | 91.6972 | 82.3440 | 8741 | 392 | 8769 | 794 | 75 | 9.4458 | |
| gduggal-bwafb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 93.6596 | 95.7079 | 91.6972 | 82.3440 | 8741 | 392 | 8769 | 794 | 75 | 9.4458 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.6665 | 93.9188 | 99.5798 | 30.8815 | 8726 | 565 | 8768 | 37 | 37 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.6665 | 93.9188 | 99.5798 | 30.8815 | 8726 | 565 | 8768 | 37 | 37 | 100.0000 | |
| egarrison-hhga | SNP | tv | HG002compoundhet | * | 98.7023 | 98.0164 | 99.3979 | 47.2112 | 8746 | 177 | 8749 | 53 | 39 | 73.5849 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.4901 | 93.6175 | 99.5447 | 31.6449 | 8698 | 593 | 8745 | 40 | 40 | 100.0000 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.4901 | 93.6175 | 99.5447 | 31.6449 | 8698 | 593 | 8745 | 40 | 40 | 100.0000 | |