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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
39051-39100 / 86044 show all | |||||||||||||||
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 41.1619 | 58.5185 | 31.7460 | 42.9003 | 79 | 56 | 60 | 129 | 126 | 97.6744 | |
| ghariani-varprowl | INDEL | D6_15 | * | * | 61.5999 | 58.5275 | 65.0128 | 56.9372 | 15271 | 10821 | 15265 | 8215 | 8072 | 98.2593 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 56.4706 | 58.5366 | 54.5455 | 79.5349 | 24 | 17 | 24 | 20 | 19 | 95.0000 | |
| qzeng-custom | SNP | * | map_l250_m1_e0 | homalt | 73.6061 | 58.5465 | 99.0960 | 88.7560 | 1442 | 1021 | 1425 | 13 | 13 | 100.0000 | |
| ckim-isaac | SNP | * | map_l125_m2_e1 | * | 73.7959 | 58.5590 | 99.7510 | 72.8548 | 27641 | 19561 | 27643 | 69 | 17 | 24.6377 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 73.5572 | 58.5593 | 98.8827 | 38.1693 | 756 | 535 | 708 | 8 | 8 | 100.0000 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 73.4050 | 58.5620 | 98.3268 | 40.8270 | 1067 | 755 | 999 | 17 | 15 | 88.2353 | |
| gduggal-bwaplat | INDEL | I1_5 | map_l100_m2_e0 | homalt | 73.7841 | 58.5687 | 99.6795 | 89.4166 | 311 | 220 | 311 | 1 | 1 | 100.0000 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 59.6850 | 58.5729 | 60.8400 | 68.6799 | 38278 | 27073 | 38154 | 24558 | 22520 | 91.7013 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 59.6850 | 58.5729 | 60.8400 | 68.6799 | 38278 | 27073 | 38154 | 24558 | 22520 | 91.7013 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 58.8795 | 58.5755 | 59.1866 | 73.4509 | 4918 | 3478 | 6913 | 4767 | 1577 | 33.0816 | |
| anovak-vg | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 63.4822 | 58.5761 | 69.2853 | 62.7923 | 2131 | 1507 | 2249 | 997 | 694 | 69.6088 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 70.1135 | 58.5834 | 87.2943 | 32.4261 | 3358 | 2374 | 19787 | 2880 | 2850 | 98.9583 | |
| egarrison-hhga | INDEL | D6_15 | map_siren | hetalt | 72.8695 | 58.5859 | 96.3636 | 78.5992 | 58 | 41 | 53 | 2 | 1 | 50.0000 | |
| gduggal-bwaplat | INDEL | * | map_l150_m1_e0 | het | 73.6223 | 58.5965 | 99.0119 | 96.3513 | 501 | 354 | 501 | 5 | 1 | 20.0000 | |
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 70.0058 | 58.6077 | 86.9078 | 48.1851 | 6070 | 4287 | 6054 | 912 | 765 | 83.8816 | |
| ckim-isaac | SNP | * | map_l150_m1_e0 | het | 73.7957 | 58.6094 | 99.6041 | 78.9632 | 11321 | 7995 | 11322 | 45 | 8 | 17.7778 | |
| ckim-isaac | SNP | ti | map_l100_m1_e0 | hetalt | 73.9130 | 58.6207 | 100.0000 | 74.2424 | 17 | 12 | 17 | 0 | 0 | ||
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 71.1860 | 58.6207 | 90.6077 | 99.6597 | 51 | 36 | 328 | 34 | 30 | 88.2353 | |
| ghariani-varprowl | INDEL | D16_PLUS | map_l100_m1_e0 | * | 59.7750 | 58.6207 | 60.9756 | 96.0271 | 51 | 36 | 50 | 32 | 22 | 68.7500 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 70.4102 | 58.6207 | 88.1356 | 99.8947 | 51 | 36 | 52 | 7 | 6 | 85.7143 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 61.4577 | 58.6207 | 64.5833 | 99.8482 | 51 | 36 | 31 | 17 | 5 | 29.4118 | |
| ckim-gatk | SNP | ti | map_l250_m1_e0 | het | 72.9254 | 58.6253 | 96.4523 | 96.6462 | 1740 | 1228 | 1740 | 64 | 8 | 12.5000 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 72.9300 | 58.6592 | 96.3768 | 29.2308 | 105 | 74 | 133 | 5 | 4 | 80.0000 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 59.6441 | 58.6663 | 60.6552 | 76.8269 | 38339 | 27012 | 38291 | 24838 | 23765 | 95.6800 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 59.6441 | 58.6663 | 60.6552 | 76.8269 | 38339 | 27012 | 38291 | 24838 | 23765 | 95.6800 | |
| ciseli-custom | INDEL | D1_5 | map_l250_m2_e0 | het | 64.0842 | 58.6777 | 70.5882 | 97.7293 | 71 | 50 | 72 | 30 | 6 | 20.0000 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 73.9583 | 58.6777 | 100.0000 | 49.7207 | 213 | 150 | 90 | 0 | 0 | ||
| jpowers-varprowl | INDEL | I6_15 | map_siren | * | 66.5799 | 58.6885 | 76.9231 | 81.1897 | 179 | 126 | 180 | 54 | 53 | 98.1481 | |
| gduggal-bwaplat | INDEL | D6_15 | map_l150_m2_e0 | het | 73.9726 | 58.6957 | 100.0000 | 97.7500 | 27 | 19 | 27 | 0 | 0 | ||
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 73.7322 | 58.7029 | 99.1053 | 30.0313 | 4752 | 3343 | 4431 | 40 | 34 | 85.0000 | |
| ckim-isaac | INDEL | D16_PLUS | HG002complexvar | hetalt | 71.9738 | 58.7045 | 92.9936 | 55.5660 | 145 | 102 | 438 | 33 | 26 | 78.7879 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 64.7519 | 58.7097 | 72.1805 | 82.7048 | 91 | 64 | 96 | 37 | 36 | 97.2973 | |
| anovak-vg | INDEL | I1_5 | map_l125_m0_e0 | * | 57.2924 | 58.7097 | 55.9420 | 90.7507 | 182 | 128 | 193 | 152 | 98 | 64.4737 | |
| jmaeng-gatk | SNP | tv | map_l250_m2_e0 | het | 72.5709 | 58.7113 | 94.9958 | 96.9665 | 1139 | 801 | 1139 | 60 | 1 | 1.6667 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 70.4500 | 58.7209 | 88.0342 | 68.5484 | 101 | 71 | 103 | 14 | 5 | 35.7143 | |
| jpowers-varprowl | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 70.1373 | 58.7236 | 87.0583 | 47.6620 | 6082 | 4275 | 6061 | 901 | 793 | 88.0133 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 58.7303 | 0.0000 | 0.0000 | 6152 | 4323 | 0 | 0 | 0 | ||
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 69.4882 | 58.7467 | 85.0365 | 91.8258 | 225 | 158 | 233 | 41 | 17 | 41.4634 | |
| jpowers-varprowl | INDEL | D16_PLUS | * | homalt | 72.0589 | 58.7470 | 93.1712 | 70.1813 | 994 | 698 | 996 | 73 | 69 | 94.5205 | |
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 72.0169 | 58.7500 | 93.0233 | 81.0095 | 282 | 198 | 280 | 21 | 14 | 66.6667 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 73.7836 | 58.7520 | 99.1512 | 28.6930 | 4011 | 2816 | 3738 | 32 | 26 | 81.2500 | |
| ghariani-varprowl | INDEL | D16_PLUS | map_l100_m2_e1 | * | 60.4431 | 58.7629 | 62.2222 | 95.9441 | 57 | 40 | 56 | 34 | 24 | 70.5882 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 69.9531 | 58.7771 | 86.3768 | 94.4057 | 298 | 209 | 298 | 47 | 23 | 48.9362 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 73.2187 | 58.7771 | 97.0684 | 92.5467 | 298 | 209 | 298 | 9 | 8 | 88.8889 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 69.2765 | 58.7912 | 84.3137 | 82.8571 | 321 | 225 | 430 | 80 | 10 | 12.5000 | |
| ghariani-varprowl | INDEL | D16_PLUS | * | homalt | 72.0773 | 58.8061 | 93.0841 | 70.1867 | 995 | 697 | 996 | 74 | 68 | 91.8919 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 58.8176 | 0.0000 | 0.0000 | 3492 | 2445 | 0 | 0 | 0 | ||
| gduggal-bwaplat | SNP | tv | map_l125_m2_e0 | * | 73.9169 | 58.8210 | 99.4361 | 88.9350 | 9699 | 6790 | 9699 | 55 | 13 | 23.6364 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 74.0741 | 58.8235 | 100.0000 | 50.0000 | 40 | 28 | 38 | 0 | 0 | ||