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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
78401-78450 / 86044 show all | |||||||||||||||
| 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 | |
| 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 | |
| jmaeng-gatk | SNP | tv | HG002compoundhet | * | 99.2678 | 98.7672 | 99.7735 | 49.6292 | 8813 | 110 | 8810 | 20 | 17 | 85.0000 | |
| cchapple-custom | SNP | tv | HG002compoundhet | * | 99.1131 | 98.7784 | 99.4501 | 47.4326 | 8814 | 109 | 9224 | 51 | 34 | 66.6667 | |
| 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 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 76.4899 | 74.2821 | 78.8329 | 50.1539 | 8821 | 3054 | 8808 | 2365 | 2266 | 95.8140 | |
| 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 | ||
| ckim-gatk | SNP | tv | HG002compoundhet | * | 99.2966 | 98.8905 | 99.7061 | 49.4688 | 8824 | 99 | 8821 | 26 | 17 | 65.3846 | |
| ckim-isaac | SNP | * | map_l125_m2_e0 | homalt | 67.3485 | 50.7856 | 99.9434 | 65.6165 | 8824 | 8551 | 8824 | 5 | 5 | 100.0000 | |
| 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 | |
| ltrigg-rtg2 | SNP | tv | HG002compoundhet | * | 99.3414 | 98.9802 | 99.7052 | 44.7928 | 8832 | 91 | 8795 | 26 | 6 | 23.0769 | |
| 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 | ||
| eyeh-varpipe | SNP | tv | HG002compoundhet | * | 97.1567 | 99.0474 | 95.3368 | 45.3099 | 8838 | 85 | 7176 | 351 | 78 | 22.2222 | |
| gduggal-bwavard | SNP | tv | map_l100_m1_e0 | homalt | 98.7927 | 97.7441 | 99.8639 | 61.4588 | 8839 | 204 | 8807 | 12 | 10 | 83.3333 | |
| 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-bwafb | SNP | tv | HG002compoundhet | * | 97.8192 | 99.1259 | 96.5465 | 53.1590 | 8845 | 78 | 8890 | 318 | 86 | 27.0440 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 77.1804 | 63.0915 | 99.3707 | 35.9250 | 8853 | 5179 | 9000 | 57 | 56 | 98.2456 | |
| gduggal-snapplat | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 92.7199 | 87.6559 | 98.4048 | 61.6199 | 8855 | 1247 | 8883 | 144 | 56 | 38.8889 | |
| 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 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.3400 | 95.3206 | 99.4468 | 70.6377 | 8861 | 435 | 8988 | 50 | 50 | 100.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.6101 | 95.3421 | 99.9887 | 62.3644 | 8863 | 433 | 8881 | 1 | 0 | 0.0000 | |
| ckim-isaac | INDEL | D1_5 | HG002compoundhet | hetalt | 92.5735 | 86.7561 | 99.2273 | 35.2319 | 8863 | 1353 | 9117 | 71 | 65 | 91.5493 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.9134 | 97.0765 | 98.7647 | 80.5287 | 8866 | 267 | 8875 | 111 | 13 | 11.7117 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.9134 | 97.0765 | 98.7647 | 80.5287 | 8866 | 267 | 8875 | 111 | 13 | 11.7117 | |
| ciseli-custom | SNP | ti | map_l150_m2_e0 | het | 74.3678 | 68.8533 | 80.8425 | 84.6368 | 8869 | 4012 | 8866 | 2101 | 62 | 2.9510 | |
| jpowers-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 87.8581 | 97.1203 | 80.2087 | 86.4645 | 8870 | 263 | 8916 | 2200 | 30 | 1.3636 | |
| jpowers-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 87.8581 | 97.1203 | 80.2087 | 86.4645 | 8870 | 263 | 8916 | 2200 | 30 | 1.3636 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 82.5030 | 79.8704 | 85.3152 | 53.3915 | 8872 | 2236 | 10353 | 1782 | 570 | 31.9865 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.3822 | 95.4389 | 99.4064 | 62.1615 | 8872 | 424 | 8875 | 53 | 52 | 98.1132 | |
| hfeng-pmm2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.2678 | 97.2079 | 99.3509 | 74.1300 | 8878 | 255 | 8878 | 58 | 4 | 6.8966 | |
| hfeng-pmm2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.2678 | 97.2079 | 99.3509 | 74.1300 | 8878 | 255 | 8878 | 58 | 4 | 6.8966 | |
| ckim-isaac | INDEL | D1_5 | * | hetalt | 92.0397 | 86.6959 | 98.0855 | 45.9935 | 8882 | 1363 | 9222 | 180 | 168 | 93.3333 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.7343 | 95.5895 | 99.9775 | 64.8179 | 8886 | 410 | 8904 | 2 | 1 | 50.0000 | |
| jlack-gatk | SNP | tv | HG002compoundhet | * | 99.3236 | 99.5965 | 99.0521 | 49.7619 | 8887 | 36 | 8882 | 85 | 24 | 28.2353 | |
| rpoplin-dv42 | SNP | tv | HG002compoundhet | * | 99.6523 | 99.5965 | 99.7081 | 48.4905 | 8887 | 36 | 8880 | 26 | 19 | 73.0769 | |
| anovak-vg | SNP | * | map_l150_m1_e0 | homalt | 87.8735 | 78.8344 | 99.2540 | 70.4677 | 8887 | 2386 | 8781 | 66 | 54 | 81.8182 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.5589 | 95.6625 | 99.5320 | 31.5275 | 8888 | 403 | 8932 | 42 | 40 | 95.2381 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.5589 | 95.6625 | 99.5320 | 31.5275 | 8888 | 403 | 8932 | 42 | 40 | 95.2381 | |
| ckim-isaac | SNP | * | HG002compoundhet | homalt | 90.1933 | 82.4430 | 99.5521 | 29.8507 | 8889 | 1893 | 8890 | 40 | 35 | 87.5000 | |
| jli-custom | SNP | tv | HG002compoundhet | * | 99.6414 | 99.6526 | 99.6301 | 48.9851 | 8892 | 31 | 8889 | 33 | 14 | 42.4242 | |
| astatham-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.4610 | 97.3722 | 99.5745 | 76.8854 | 8893 | 240 | 8893 | 38 | 10 | 26.3158 | |
| astatham-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.4610 | 97.3722 | 99.5745 | 76.8854 | 8893 | 240 | 8893 | 38 | 10 | 26.3158 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 95.7078 | 0.0000 | 0.0000 | 8897 | 399 | 0 | 0 | 0 | ||
| raldana-dualsentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.2933 | 97.4269 | 99.1752 | 74.7089 | 8898 | 235 | 8898 | 74 | 10 | 13.5135 | |
| raldana-dualsentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.2933 | 97.4269 | 99.1752 | 74.7089 | 8898 | 235 | 8898 | 74 | 10 | 13.5135 | |
| ckim-vqsr | SNP | tv | map_l125_m2_e0 | * | 69.7523 | 53.9693 | 98.5819 | 89.6043 | 8899 | 7590 | 8898 | 128 | 1 | 0.7813 | |
| ckim-dragen | SNP | tv | HG002compoundhet | * | 99.7984 | 99.7422 | 99.8546 | 49.3913 | 8900 | 23 | 8925 | 13 | 8 | 61.5385 | |