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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
3351-3400 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | * | * | hetalt | 94.2358 | 89.4005 | 99.6240 | 58.0561 | 22562 | 2675 | 22786 | 86 | 78 | 90.6977 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 63.5899 | 54.1867 | 76.9418 | 62.7693 | 19828 | 16764 | 22724 | 6810 | 2991 | 43.9207 | |
| jmaeng-gatk | SNP | ti | map_l125_m2_e0 | * | 85.0261 | 75.0281 | 98.0984 | 84.6739 | 22702 | 7556 | 22698 | 440 | 41 | 9.3182 | |
| ckim-gatk | SNP | ti | map_l125_m2_e0 | * | 85.0542 | 75.0248 | 98.1789 | 84.5122 | 22701 | 7557 | 22697 | 421 | 45 | 10.6888 | |
| anovak-vg | SNP | * | map_l100_m1_e0 | homalt | 91.6965 | 85.1461 | 99.3387 | 58.6113 | 22992 | 4011 | 22684 | 151 | 130 | 86.0927 | |
| astatham-gatk | SNP | tv | map_siren | het | 88.3820 | 79.2932 | 99.8239 | 66.9200 | 22685 | 5924 | 22680 | 40 | 11 | 27.5000 | |
| jlack-gatk | INDEL | * | HG002compoundhet | hetalt | 94.2807 | 89.4162 | 99.7049 | 50.9823 | 22515 | 2665 | 22637 | 67 | 62 | 92.5373 | |
| asubramanian-gatk | SNP | ti | map_l100_m2_e1 | * | 62.6607 | 45.6542 | 99.8585 | 84.1129 | 22592 | 26893 | 22588 | 32 | 12 | 37.5000 | |
| anovak-vg | SNP | tv | map_l100_m2_e1 | * | 83.6965 | 89.4751 | 78.6189 | 71.8943 | 22622 | 2661 | 22577 | 6140 | 1324 | 21.5635 | |
| ckim-vqsr | SNP | ti | map_l100_m1_e0 | het | 85.6453 | 75.3523 | 99.1953 | 82.9534 | 22562 | 7380 | 22557 | 183 | 10 | 5.4645 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 54.6126 | 50.3907 | 59.6067 | 38.4218 | 16121 | 15871 | 22551 | 15282 | 11968 | 78.3144 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 61.6156 | 61.1636 | 62.0744 | 51.1512 | 22381 | 14211 | 22533 | 13767 | 10331 | 75.0418 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 93.9157 | 91.6952 | 96.2464 | 33.3267 | 22502 | 2038 | 22436 | 875 | 753 | 86.0571 | |
| mlin-fermikit | INDEL | D6_15 | * | * | 87.9258 | 85.7734 | 90.1891 | 52.9541 | 22380 | 3712 | 22421 | 2439 | 2392 | 98.0730 | |
| ciseli-custom | SNP | * | map_l150_m1_e0 | * | 77.9234 | 73.3052 | 83.1626 | 80.2472 | 22438 | 8171 | 22404 | 4536 | 1124 | 24.7795 | |
| qzeng-custom | SNP | * | map_l150_m2_e1 | * | 81.4031 | 70.2204 | 96.8222 | 87.0167 | 22618 | 9592 | 22364 | 734 | 626 | 85.2861 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 92.2240 | 99.4840 | 85.9515 | 72.5594 | 21786 | 113 | 22362 | 3655 | 3631 | 99.3434 | |
| anovak-vg | SNP | tv | map_l100_m2_e0 | * | 83.6288 | 89.4260 | 78.5375 | 71.8835 | 22386 | 2647 | 22351 | 6108 | 1319 | 21.5946 | |
| astatham-gatk | SNP | * | map_l125_m2_e1 | het | 85.8279 | 75.3644 | 99.6653 | 80.7852 | 22338 | 7302 | 22332 | 75 | 27 | 36.0000 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 70.9708 | 71.4018 | 70.5450 | 38.3153 | 17522 | 7018 | 22276 | 9301 | 8410 | 90.4204 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 93.4170 | 87.7992 | 99.8027 | 58.9642 | 22265 | 3094 | 22261 | 44 | 35 | 79.5455 | |
| jpowers-varprowl | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 81.7040 | 72.4326 | 93.6973 | 66.4963 | 22281 | 8480 | 22240 | 1496 | 1307 | 87.3663 | |
| jmaeng-gatk | SNP | * | map_l150_m2_e1 | * | 80.8313 | 69.0469 | 97.4662 | 88.8350 | 22240 | 9970 | 22234 | 578 | 42 | 7.2664 | |
| asubramanian-gatk | SNP | ti | map_l100_m2_e0 | * | 62.4314 | 45.4117 | 99.8563 | 84.1830 | 22234 | 26727 | 22230 | 32 | 12 | 37.5000 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 92.8911 | 87.3497 | 99.1833 | 60.3693 | 22151 | 3208 | 22225 | 183 | 36 | 19.6721 | |
| ghariani-varprowl | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 81.5331 | 72.3481 | 93.3894 | 66.7128 | 22255 | 8506 | 22222 | 1573 | 1272 | 80.8646 | |
| ckim-gatk | SNP | * | map_l150_m2_e1 | * | 80.8459 | 69.0003 | 97.6016 | 88.7044 | 22225 | 9985 | 22219 | 546 | 44 | 8.0586 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.5436 | 96.2382 | 98.8849 | 41.9802 | 21413 | 837 | 22170 | 250 | 228 | 91.2000 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.0261 | 98.9819 | 99.0704 | 52.1206 | 11181 | 115 | 22167 | 208 | 201 | 96.6346 | |
| mlin-fermikit | SNP | * | map_l125_m1_e0 | * | 62.6787 | 48.9002 | 87.2681 | 57.2976 | 22165 | 23162 | 22160 | 3233 | 2859 | 88.4318 | |
| asubramanian-gatk | SNP | * | map_l100_m2_e1 | het | 64.0057 | 47.1171 | 99.7652 | 87.0062 | 22097 | 24801 | 22091 | 52 | 14 | 26.9231 | |
| astatham-gatk | SNP | * | map_l125_m2_e0 | het | 85.8236 | 75.3598 | 99.6616 | 80.7499 | 22094 | 7224 | 22088 | 75 | 27 | 36.0000 | |
| qzeng-custom | SNP | * | map_l150_m2_e0 | * | 81.2952 | 70.0678 | 96.8072 | 87.0114 | 22318 | 9534 | 22073 | 728 | 620 | 85.1648 | |
| qzeng-custom | SNP | ti | map_l125_m2_e1 | * | 83.3343 | 72.6815 | 97.6462 | 82.9373 | 22218 | 8351 | 22070 | 532 | 443 | 83.2707 | |
| ckim-isaac | SNP | ti | map_l100_m2_e1 | het | 83.1462 | 71.2597 | 99.7920 | 67.1300 | 22062 | 8898 | 22066 | 46 | 4 | 8.6957 | |
| ciseli-custom | SNP | * | HG002compoundhet | * | 73.2436 | 85.0050 | 64.3413 | 46.5864 | 21950 | 3872 | 21988 | 12186 | 1203 | 9.8720 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 80.7791 | 74.7144 | 87.9154 | 43.6787 | 10921 | 3696 | 21956 | 3018 | 1053 | 34.8907 | |
| jmaeng-gatk | SNP | * | map_l150_m2_e0 | * | 80.7195 | 68.8748 | 97.4842 | 88.8293 | 21938 | 9914 | 21932 | 566 | 41 | 7.2438 | |
| ckim-gatk | SNP | * | map_l150_m2_e0 | * | 80.7304 | 68.8246 | 97.6170 | 88.6980 | 21922 | 9930 | 21916 | 535 | 43 | 8.0374 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6721 | 99.9543 | 99.3915 | 75.2467 | 21889 | 10 | 21889 | 134 | 133 | 99.2537 | |
| qzeng-custom | SNP | * | map_l125_m2_e1 | het | 84.1292 | 74.4636 | 96.6784 | 86.6172 | 22071 | 7569 | 21888 | 752 | 615 | 81.7819 | |
| jli-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.8267 | 99.9315 | 99.7221 | 75.0916 | 21884 | 15 | 21888 | 61 | 59 | 96.7213 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.7221 | 99.9452 | 99.4999 | 76.1475 | 21887 | 12 | 21887 | 110 | 109 | 99.0909 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5837 | 99.9406 | 99.2292 | 75.9456 | 21886 | 13 | 21886 | 170 | 169 | 99.4118 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.7061 | 99.9315 | 99.4818 | 75.9939 | 21884 | 15 | 21884 | 114 | 113 | 99.1228 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6970 | 99.9315 | 99.4637 | 76.0277 | 21884 | 15 | 21884 | 118 | 117 | 99.1525 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6721 | 99.9315 | 99.4140 | 76.0962 | 21884 | 15 | 21884 | 129 | 128 | 99.2248 | |
| gduggal-snapvard | INDEL | * | HG002complexvar | homalt | 88.0378 | 80.0821 | 97.7484 | 41.5287 | 21643 | 5383 | 21880 | 504 | 456 | 90.4762 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6856 | 99.9087 | 99.4636 | 76.0319 | 21879 | 20 | 21879 | 118 | 117 | 99.1525 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4496 | 99.8356 | 99.0666 | 73.6565 | 21863 | 36 | 21863 | 206 | 205 | 99.5146 | |