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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
1751-1800 / 86044 show all | |||||||||||||||
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 91.6563 | 86.8570 | 97.0171 | 59.4271 | 26474 | 4006 | 42997 | 1322 | 971 | 73.4493 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 91.6563 | 86.8570 | 97.0171 | 59.4271 | 26474 | 4006 | 42997 | 1322 | 971 | 73.4493 | |
| ciseli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 82.0846 | 86.7638 | 77.8844 | 75.9358 | 41880 | 6389 | 42785 | 12149 | 5113 | 42.0858 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1729 | 98.6761 | 99.6748 | 69.3950 | 32796 | 440 | 42603 | 139 | 118 | 84.8921 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 77.5469 | 65.0258 | 96.0400 | 78.6649 | 42495 | 22856 | 42490 | 1752 | 879 | 50.1712 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 77.5469 | 65.0258 | 96.0400 | 78.6649 | 42495 | 22856 | 42490 | 1752 | 879 | 50.1712 | |
| astatham-gatk | SNP | ti | map_l100_m2_e1 | * | 92.0971 | 85.4623 | 99.8489 | 69.7778 | 42291 | 7194 | 42284 | 64 | 36 | 56.2500 | |
| anovak-vg | SNP | * | map_l100_m2_e1 | het | 80.7046 | 91.1126 | 72.4307 | 73.6475 | 42730 | 4168 | 42251 | 16082 | 3449 | 21.4463 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.0559 | 96.7947 | 99.3503 | 55.8922 | 41946 | 1389 | 42206 | 276 | 166 | 60.1449 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.8990 | 97.6739 | 98.1251 | 62.1451 | 42327 | 1008 | 42130 | 805 | 744 | 92.4224 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.8510 | 97.6024 | 98.1008 | 61.8066 | 42296 | 1039 | 42098 | 815 | 759 | 93.1288 | |
| anovak-vg | SNP | ti | map_l100_m1_e0 | * | 84.3963 | 88.5106 | 80.6475 | 68.7475 | 42424 | 5507 | 42052 | 10091 | 2274 | 22.5349 | |
| eyeh-varpipe | INDEL | * | HG002complexvar | het | 95.5256 | 94.2569 | 96.8290 | 49.4429 | 43558 | 2654 | 42048 | 1377 | 1284 | 93.2462 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 94.5069 | 96.4277 | 92.6612 | 46.2676 | 15197 | 563 | 42020 | 3328 | 2198 | 66.0457 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.0520 | 97.3439 | 98.7704 | 57.5661 | 42184 | 1151 | 42011 | 523 | 468 | 89.4837 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.4475 | 97.1963 | 97.6999 | 61.5897 | 42120 | 1215 | 41925 | 987 | 925 | 93.7183 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.6448 | 97.1963 | 98.0976 | 61.8032 | 42120 | 1215 | 41922 | 813 | 755 | 92.8659 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.6262 | 97.1247 | 98.1330 | 61.8291 | 42089 | 1246 | 41891 | 797 | 748 | 93.8519 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.4130 | 97.1455 | 97.6820 | 62.4233 | 42098 | 1237 | 41887 | 994 | 949 | 95.4728 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 71.2051 | 68.6858 | 73.9162 | 57.7097 | 29765 | 13570 | 41841 | 14765 | 14397 | 97.5076 | |
| astatham-gatk | SNP | ti | map_l100_m2_e0 | * | 92.0782 | 85.4292 | 99.8496 | 69.7884 | 41827 | 7134 | 41820 | 63 | 36 | 57.1429 | |
| anovak-vg | SNP | * | map_l100_m2_e0 | het | 80.6158 | 91.0795 | 72.3085 | 73.6388 | 42260 | 4139 | 41790 | 16004 | 3433 | 21.4509 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.6704 | 98.1255 | 97.2195 | 71.9856 | 32613 | 623 | 41783 | 1195 | 869 | 72.7197 | |
| anovak-vg | SNP | tv | map_siren | * | 87.1130 | 91.2040 | 83.3733 | 62.1288 | 41890 | 4040 | 41755 | 8327 | 1807 | 21.7005 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.4052 | 96.7970 | 98.0210 | 61.6169 | 41947 | 1388 | 41755 | 843 | 795 | 94.3060 | |
| gduggal-bwaplat | SNP | * | map_siren | homalt | 86.1632 | 75.7053 | 99.9736 | 58.6738 | 41756 | 13400 | 41721 | 11 | 9 | 81.8182 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 94.3555 | 90.6219 | 98.4100 | 63.4241 | 41416 | 4286 | 41653 | 673 | 294 | 43.6850 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 94.3555 | 90.6219 | 98.4100 | 63.4241 | 41416 | 4286 | 41653 | 673 | 294 | 43.6850 | |
| asubramanian-gatk | SNP | ti | map_siren | het | 80.0204 | 66.7709 | 99.8298 | 71.1364 | 41653 | 20729 | 41647 | 71 | 23 | 32.3944 | |
| gduggal-snapplat | SNP | * | map_l125_m1_e0 | * | 93.8560 | 91.8106 | 95.9947 | 80.5503 | 41615 | 3712 | 41630 | 1737 | 931 | 53.5982 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.3588 | 95.3386 | 99.4664 | 56.7621 | 41315 | 2020 | 41569 | 223 | 143 | 64.1256 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 93.4281 | 91.8537 | 95.0573 | 78.9460 | 41979 | 3723 | 41502 | 2158 | 356 | 16.4968 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 93.4281 | 91.8537 | 95.0573 | 78.9460 | 41979 | 3723 | 41502 | 2158 | 356 | 16.4968 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.5538 | 96.1694 | 98.9788 | 57.8031 | 41675 | 1660 | 41482 | 428 | 360 | 84.1121 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.5003 | 96.1325 | 98.9076 | 58.5444 | 41659 | 1676 | 41469 | 458 | 399 | 87.1179 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.2804 | 95.7563 | 96.8102 | 77.5473 | 41496 | 1839 | 41428 | 1365 | 1297 | 95.0183 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9358 | 97.0774 | 98.8095 | 45.2536 | 31057 | 935 | 41417 | 499 | 447 | 89.5792 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.4936 | 95.9940 | 99.0408 | 57.8182 | 41599 | 1736 | 41405 | 401 | 351 | 87.5312 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.8420 | 95.6294 | 98.0857 | 58.9442 | 41441 | 1894 | 41248 | 805 | 768 | 95.4037 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.1122 | 95.6040 | 96.6259 | 60.2914 | 41430 | 1905 | 41238 | 1440 | 1303 | 90.4861 | |
| ckim-gatk | SNP | * | map_l100_m2_e1 | het | 92.4550 | 87.9526 | 97.4432 | 82.5075 | 41248 | 5650 | 41237 | 1082 | 78 | 7.2089 | |
| jmaeng-gatk | SNP | * | map_l100_m2_e1 | het | 92.3544 | 87.8737 | 97.3167 | 82.8441 | 41211 | 5687 | 41200 | 1136 | 70 | 6.1620 | |
| ciseli-custom | SNP | ti | map_l100_m2_e1 | * | 86.3257 | 83.3424 | 89.5306 | 71.0284 | 41242 | 8243 | 41176 | 4815 | 1336 | 27.7466 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 87.0050 | 91.1424 | 83.2268 | 80.9890 | 41653 | 4048 | 41154 | 8294 | 340 | 4.0994 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 87.0050 | 91.1424 | 83.2268 | 80.9890 | 41653 | 4048 | 41154 | 8294 | 340 | 4.0994 | |
| ckim-gatk | SNP | ti | map_l100_m2_e1 | * | 90.0482 | 82.8877 | 98.5628 | 78.3843 | 41017 | 8468 | 41010 | 598 | 70 | 11.7057 | |
| jmaeng-gatk | SNP | ti | map_l100_m2_e1 | * | 90.0240 | 82.8837 | 98.5106 | 78.5961 | 41015 | 8470 | 41008 | 620 | 64 | 10.3226 | |
| astatham-gatk | SNP | ti | map_l100_m1_e0 | * | 92.0088 | 85.3122 | 99.8461 | 68.2409 | 40891 | 7040 | 40884 | 63 | 36 | 57.1429 | |
| anovak-vg | SNP | * | map_l100_m1_e0 | het | 80.4155 | 91.0315 | 72.0169 | 72.1565 | 41291 | 4068 | 40830 | 15865 | 3407 | 21.4749 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 65.2231 | 63.7325 | 66.7851 | 42.6875 | 23321 | 13271 | 40773 | 20278 | 18291 | 90.2012 | |