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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
56351-56400 / 86044 show all | |||||||||||||||
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.5930 | 99.2105 | 97.9830 | 63.7025 | 8294 | 66 | 8307 | 171 | 160 | 93.5673 | |
| jli-custom | INDEL | D1_5 | map_l125_m0_e0 | * | 97.9839 | 97.9839 | 97.9839 | 87.4399 | 486 | 10 | 486 | 10 | 3 | 30.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l125_m0_e0 | * | 97.8830 | 97.7823 | 97.9839 | 88.0998 | 485 | 11 | 486 | 10 | 4 | 40.0000 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.7158 | 97.4490 | 97.9841 | 76.9231 | 2101 | 55 | 2090 | 43 | 21 | 48.8372 | |
| ckim-gatk | SNP | ti | map_l150_m1_e0 | * | 80.5127 | 68.3289 | 97.9843 | 87.5524 | 13469 | 6243 | 13465 | 277 | 34 | 12.2744 | |
| raldana-dualsentieon | INDEL | I1_5 | map_l100_m0_e0 | * | 98.0718 | 98.1584 | 97.9853 | 81.8544 | 533 | 10 | 535 | 11 | 1 | 9.0909 | |
| jli-custom | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.7437 | 95.5319 | 97.9866 | 71.7029 | 1347 | 63 | 1314 | 27 | 20 | 74.0741 | |
| asubramanian-gatk | INDEL | I1_5 | map_l125_m2_e1 | * | 90.3357 | 83.7931 | 97.9866 | 90.5301 | 729 | 141 | 730 | 15 | 1 | 6.6667 | |
| dgrover-gatk | SNP | ti | map_l250_m1_e0 | het | 98.2014 | 98.4164 | 97.9873 | 91.3429 | 2921 | 47 | 2921 | 60 | 16 | 26.6667 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.3732 | 96.7655 | 97.9885 | 73.3129 | 718 | 24 | 682 | 14 | 9 | 64.2857 | |
| ckim-isaac | INDEL | * | map_l100_m2_e0 | het | 84.2881 | 73.9489 | 97.9885 | 86.2255 | 1706 | 601 | 1705 | 35 | 15 | 42.8571 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 92.0166 | 86.7307 | 97.9886 | 88.3681 | 16981 | 2598 | 17002 | 349 | 101 | 28.9398 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 92.0166 | 86.7307 | 97.9886 | 88.3681 | 16981 | 2598 | 17002 | 349 | 101 | 28.9398 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.9538 | 99.9378 | 97.9890 | 60.2085 | 1608 | 1 | 1608 | 33 | 18 | 54.5455 | |
| ltrigg-rtg1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.8848 | 99.7965 | 97.9897 | 57.5988 | 3923 | 8 | 3997 | 82 | 1 | 1.2195 | |
| gduggal-bwavard | INDEL | I1_5 | map_l100_m0_e0 | homalt | 96.3229 | 94.7115 | 97.9899 | 73.6074 | 197 | 11 | 195 | 4 | 2 | 50.0000 | |
| raldana-dualsentieon | INDEL | * | map_l150_m2_e0 | * | 97.3214 | 96.6619 | 97.9899 | 88.6072 | 1361 | 47 | 1365 | 28 | 4 | 14.2857 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 96.2963 | 94.6602 | 97.9899 | 88.0409 | 195 | 11 | 195 | 4 | 2 | 50.0000 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.8387 | 93.7799 | 97.9899 | 66.6107 | 196 | 13 | 195 | 4 | 4 | 100.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 96.8124 | 95.6628 | 97.9899 | 63.3939 | 3132 | 142 | 3120 | 64 | 61 | 95.3125 | |
| dgrover-gatk | INDEL | * | map_l150_m2_e1 | * | 97.9875 | 97.9847 | 97.9903 | 91.3313 | 1410 | 29 | 1414 | 29 | 7 | 24.1379 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.8395 | 97.6888 | 97.9907 | 65.9474 | 634 | 15 | 634 | 13 | 13 | 100.0000 | |
| ckim-gatk | SNP | ti | map_l150_m2_e1 | * | 81.3077 | 69.4784 | 97.9917 | 88.2788 | 14398 | 6325 | 14394 | 295 | 35 | 11.8644 | |
| ndellapenna-hhga | INDEL | * | HG002complexvar | het | 97.4850 | 96.9835 | 97.9917 | 54.0711 | 44818 | 1394 | 44840 | 919 | 671 | 73.0141 | |
| ltrigg-rtg2 | INDEL | D6_15 | map_l100_m2_e0 | * | 96.1200 | 94.3182 | 97.9920 | 81.1364 | 249 | 15 | 244 | 5 | 0 | 0.0000 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 96.6872 | 95.4167 | 97.9920 | 85.6042 | 687 | 33 | 732 | 15 | 12 | 80.0000 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.9211 | 97.8503 | 97.9920 | 79.1387 | 1229 | 27 | 1220 | 25 | 7 | 28.0000 | |
| raldana-dualsentieon | SNP | ti | map_l250_m2_e0 | * | 98.2170 | 98.4425 | 97.9924 | 88.3517 | 4930 | 78 | 4930 | 101 | 3 | 2.9703 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 86.6815 | 77.7114 | 97.9925 | 71.6067 | 781 | 224 | 781 | 16 | 10 | 62.5000 | |
| jpowers-varprowl | SNP | * | map_l125_m2_e0 | * | 97.5865 | 97.1834 | 97.9930 | 76.8491 | 45407 | 1316 | 45407 | 930 | 284 | 30.5376 | |
| bgallagher-sentieon | INDEL | I1_5 | map_l150_m1_e0 | het | 97.6577 | 97.3244 | 97.9933 | 90.1645 | 291 | 8 | 293 | 6 | 0 | 0.0000 | |
| ckim-vqsr | SNP | ti | map_l250_m1_e0 | het | 68.5076 | 52.6617 | 97.9937 | 97.0232 | 1563 | 1405 | 1563 | 32 | 0 | 0.0000 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 97.8552 | 97.7169 | 97.9938 | 73.0000 | 642 | 15 | 635 | 13 | 12 | 92.3077 | |
| ckim-gatk | SNP | ti | map_l150_m2_e0 | * | 81.1968 | 69.3155 | 97.9938 | 88.2579 | 14218 | 6294 | 14214 | 291 | 35 | 12.0275 | |
| ltrigg-rtg2 | INDEL | * | HG002complexvar | hetalt | 95.5730 | 93.2685 | 97.9943 | 75.0000 | 3450 | 249 | 4153 | 85 | 84 | 98.8235 | |
| dgrover-gatk | INDEL | * | map_l125_m2_e0 | het | 98.0266 | 98.0590 | 97.9943 | 89.7744 | 1364 | 27 | 1368 | 28 | 4 | 14.2857 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.9145 | 97.8347 | 97.9944 | 55.0665 | 4202 | 93 | 4202 | 86 | 37 | 43.0233 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.4365 | 96.8847 | 97.9946 | 71.7201 | 6220 | 200 | 6206 | 127 | 19 | 14.9606 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.4365 | 96.8847 | 97.9946 | 71.7201 | 6220 | 200 | 6206 | 127 | 19 | 14.9606 | |
| gduggal-snapvard | SNP | tv | HG002compoundhet | homalt | 90.8698 | 84.7107 | 97.9946 | 41.8088 | 2870 | 518 | 2541 | 52 | 38 | 73.0769 | |
| mlin-fermikit | SNP | tv | map_l125_m2_e1 | het | 61.6520 | 44.9730 | 97.9955 | 67.0300 | 4746 | 5807 | 4742 | 97 | 1 | 1.0309 | |
| mlin-fermikit | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.8660 | 97.7360 | 97.9964 | 54.8200 | 27326 | 633 | 27341 | 559 | 392 | 70.1252 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.3867 | 94.8287 | 97.9968 | 59.1527 | 3044 | 166 | 3033 | 62 | 60 | 96.7742 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.9969 | 97.9969 | 97.9969 | 65.7700 | 636 | 13 | 636 | 13 | 13 | 100.0000 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.9267 | 99.8738 | 97.9975 | 50.0103 | 4747 | 6 | 4747 | 97 | 96 | 98.9691 | |
| qzeng-custom | SNP | ti | segdup | het | 98.3988 | 98.8030 | 97.9978 | 93.2216 | 11886 | 144 | 11845 | 242 | 6 | 2.4793 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.2206 | 92.5954 | 97.9989 | 55.8475 | 3689 | 295 | 3722 | 76 | 35 | 46.0526 | |
| ckim-dragen | INDEL | I6_15 | * | * | 97.2249 | 96.4630 | 97.9990 | 52.8733 | 23945 | 878 | 23949 | 489 | 448 | 91.6155 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.4683 | 94.9844 | 97.9994 | 58.6524 | 3049 | 161 | 3037 | 62 | 60 | 96.7742 | |
| gduggal-bwafb | SNP | * | map_l150_m1_e0 | het | 98.1968 | 98.3951 | 97.9994 | 78.1832 | 19006 | 310 | 19006 | 388 | 96 | 24.7423 | |