PrecisionFDA
Truth Challenge
Engage and improve DNA test results with our community challenges
Explore HG002 comparison results
Use this interactive explorer to filter all results across submission entries and multiple dimensions.
| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
83001-83050 / 86044 show all | |||||||||||||||
| gduggal-snapplat | SNP | * | map_l100_m2_e1 | homalt | 95.9332 | 92.2507 | 99.9220 | 63.8706 | 25642 | 2154 | 25625 | 20 | 15 | 75.0000 | |
| cchapple-custom | INDEL | I6_15 | * | * | 97.7435 | 96.8215 | 98.6833 | 49.3635 | 24034 | 789 | 25632 | 342 | 305 | 89.1813 | |
| astatham-gatk | SNP | ti | map_l125_m2_e1 | * | 91.2494 | 84.0525 | 99.7941 | 76.0425 | 25694 | 4875 | 25690 | 53 | 29 | 54.7170 | |
| gduggal-bwafb | SNP | * | HG002compoundhet | * | 97.9194 | 99.0744 | 96.7911 | 45.9764 | 25583 | 239 | 25699 | 852 | 222 | 26.0563 | |
| rpoplin-dv42 | SNP | * | HG002compoundhet | * | 99.6493 | 99.5895 | 99.7091 | 40.7188 | 25716 | 106 | 25707 | 75 | 61 | 81.3333 | |
| jlack-gatk | SNP | * | HG002compoundhet | * | 99.5417 | 99.7018 | 99.3822 | 42.1778 | 25745 | 77 | 25738 | 160 | 46 | 28.7500 | |
| jli-custom | SNP | * | HG002compoundhet | * | 99.7328 | 99.7599 | 99.7058 | 41.1267 | 25760 | 62 | 25757 | 76 | 36 | 47.3684 | |
| bgallagher-sentieon | SNP | * | HG002compoundhet | * | 99.8063 | 99.8025 | 99.8102 | 41.0420 | 25771 | 51 | 25764 | 49 | 25 | 51.0204 | |
| dgrover-gatk | SNP | * | HG002compoundhet | * | 99.8063 | 99.8102 | 99.8025 | 41.2435 | 25773 | 49 | 25766 | 51 | 36 | 70.5882 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 92.5067 | 90.7170 | 94.3684 | 38.1735 | 14297 | 1463 | 25772 | 1538 | 1472 | 95.7087 | |
| ckim-dragen | SNP | * | HG002compoundhet | * | 99.7929 | 99.7831 | 99.8027 | 41.5217 | 25766 | 56 | 25804 | 51 | 26 | 50.9804 | |
| astatham-gatk | SNP | * | map_l150_m1_e0 | * | 91.4460 | 84.4686 | 99.6799 | 78.7872 | 25855 | 4754 | 25849 | 83 | 39 | 46.9880 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 82.8791 | 91.0940 | 76.0233 | 83.7724 | 26154 | 2557 | 25854 | 8154 | 268 | 3.2867 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 82.8791 | 91.0940 | 76.0233 | 83.7724 | 26154 | 2557 | 25854 | 8154 | 268 | 3.2867 | |
| gduggal-bwavard | SNP | * | map_l100_m1_e0 | homalt | 98.6152 | 97.3744 | 99.8881 | 60.4751 | 26294 | 709 | 25878 | 29 | 23 | 79.3103 | |
| ckim-vqsr | SNP | * | map_l125_m2_e1 | * | 70.6297 | 54.9235 | 98.9163 | 88.7326 | 25925 | 21277 | 25922 | 284 | 6 | 2.1127 | |
| mlin-fermikit | INDEL | * | HG002complexvar | homalt | 95.7600 | 96.3222 | 95.2043 | 55.1307 | 26033 | 994 | 25927 | 1306 | 1267 | 97.0138 | |
| anovak-vg | INDEL | * | HG002complexvar | homalt | 75.7278 | 94.2021 | 63.3115 | 49.8629 | 25460 | 1567 | 25940 | 15032 | 14199 | 94.4585 | |
| eyeh-varpipe | SNP | * | map_l100_m1_e0 | homalt | 99.8701 | 99.8556 | 99.8846 | 63.0607 | 26964 | 39 | 25962 | 30 | 16 | 53.3333 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 89.4545 | 89.1929 | 89.7177 | 61.8267 | 27186 | 3294 | 25967 | 2976 | 2168 | 72.8495 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 89.4545 | 89.1929 | 89.7177 | 61.8267 | 27186 | 3294 | 25967 | 2976 | 2168 | 72.8495 | |
| anovak-vg | SNP | * | map_l150_m1_e0 | * | 79.3251 | 85.8375 | 73.7311 | 78.7422 | 26274 | 4335 | 25974 | 9254 | 2118 | 22.8874 | |
| asubramanian-gatk | SNP | tv | map_siren | * | 72.2865 | 56.6449 | 99.8618 | 75.5276 | 26017 | 19913 | 26011 | 36 | 12 | 33.3333 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 92.1518 | 91.8431 | 92.4625 | 82.8802 | 26370 | 2342 | 26055 | 2124 | 340 | 16.0075 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 92.1518 | 91.8431 | 92.4625 | 82.8802 | 26370 | 2342 | 26055 | 2124 | 340 | 16.0075 | |
| ckim-isaac | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.1945 | 93.5761 | 98.9636 | 58.8872 | 25900 | 1778 | 26068 | 273 | 187 | 68.4982 | |
| eyeh-varpipe | INDEL | * | HG002complexvar | homalt | 93.9842 | 95.4231 | 92.5880 | 51.8445 | 25790 | 1237 | 26070 | 2087 | 2039 | 97.7000 | |
| anovak-vg | SNP | ti | map_l125_m2_e0 | * | 81.4788 | 86.9291 | 76.6717 | 75.9478 | 26303 | 3955 | 26086 | 7937 | 1770 | 22.3006 | |
| gduggal-snapvard | SNP | * | map_l100_m2_e0 | homalt | 98.0484 | 96.3703 | 99.7860 | 62.8472 | 26524 | 999 | 26107 | 56 | 43 | 76.7857 | |
| mlin-fermikit | SNP | * | map_l100_m2_e0 | het | 71.6803 | 56.3051 | 98.6068 | 57.9033 | 26125 | 20274 | 26117 | 369 | 11 | 2.9810 | |
| eyeh-varpipe | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.1234 | 99.6134 | 96.6774 | 60.9972 | 27571 | 107 | 26129 | 898 | 85 | 9.4655 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 94.2166 | 90.2898 | 98.5006 | 65.6575 | 25924 | 2788 | 26146 | 398 | 31 | 7.7889 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 94.2166 | 90.2898 | 98.5006 | 65.6575 | 25924 | 2788 | 26146 | 398 | 31 | 7.7889 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 91.5338 | 92.8273 | 90.2759 | 58.4295 | 26233 | 2027 | 26180 | 2820 | 1567 | 55.5674 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 65.7740 | 85.6857 | 53.3715 | 63.8640 | 26117 | 4363 | 26223 | 22910 | 22642 | 98.8302 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 65.7740 | 85.6857 | 53.3715 | 63.8640 | 26117 | 4363 | 26223 | 22910 | 22642 | 98.8302 | |
| gduggal-snapfb | SNP | * | map_l100_m1_e0 | homalt | 98.4097 | 97.1633 | 99.6885 | 68.9633 | 26237 | 766 | 26239 | 82 | 29 | 35.3659 | |
| ckim-isaac | SNP | * | map_l125_m1_e0 | * | 73.2800 | 57.9125 | 99.7492 | 70.8000 | 26250 | 19077 | 26252 | 66 | 16 | 24.2424 | |
| anovak-vg | SNP | * | map_l125_m2_e0 | het | 77.4707 | 90.4768 | 67.7339 | 78.1138 | 26526 | 2792 | 26255 | 12507 | 2731 | 21.8358 | |
| jmaeng-gatk | SNP | ti | map_l100_m1_e0 | het | 92.5822 | 87.8732 | 97.8244 | 80.8303 | 26311 | 3631 | 26304 | 585 | 55 | 9.4017 | |
| cchapple-custom | SNP | * | map_l100_m1_e0 | homalt | 98.7154 | 97.4707 | 99.9924 | 55.8509 | 26320 | 683 | 26310 | 2 | 2 | 100.0000 | |
| gduggal-bwafb | INDEL | * | HG002complexvar | homalt | 97.6327 | 97.4544 | 97.8116 | 53.5251 | 26339 | 688 | 26326 | 589 | 564 | 95.7555 | |
| gduggal-snapvard | SNP | * | map_l100_m2_e1 | homalt | 98.0418 | 96.3556 | 99.7880 | 62.8493 | 26783 | 1013 | 26357 | 56 | 43 | 76.7857 | |
| ckim-gatk | SNP | ti | map_l100_m1_e0 | het | 92.7314 | 88.0536 | 97.9342 | 80.4366 | 26365 | 3577 | 26358 | 556 | 60 | 10.7914 | |
| anovak-vg | SNP | ti | map_l125_m2_e1 | * | 81.5574 | 87.0097 | 76.7480 | 75.9636 | 26598 | 3971 | 26376 | 7991 | 1774 | 22.2000 | |
| gduggal-bwavard | SNP | * | map_l100_m2_e0 | homalt | 98.6138 | 97.3767 | 99.8826 | 62.7969 | 26801 | 722 | 26381 | 31 | 25 | 80.6452 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 87.9792 | 79.5523 | 98.4030 | 81.3702 | 26440 | 6796 | 26434 | 429 | 144 | 33.5664 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 94.8647 | 92.1636 | 97.7290 | 70.8955 | 26462 | 2250 | 26465 | 615 | 21 | 3.4146 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 94.8647 | 92.1636 | 97.7290 | 70.8955 | 26462 | 2250 | 26465 | 615 | 21 | 3.4146 | |
| eyeh-varpipe | SNP | * | map_l100_m2_e0 | homalt | 99.8725 | 99.8583 | 99.8868 | 65.3085 | 27484 | 39 | 26466 | 30 | 16 | 53.3333 | |