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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
11251-11300 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | I16_PLUS | * | * | 97.2630 | 96.1267 | 98.4265 | 70.8795 | 6130 | 247 | 6130 | 98 | 83 | 84.6939 | |
| egarrison-hhga | INDEL | D16_PLUS | HG002complexvar | * | 85.7883 | 79.5496 | 93.0889 | 62.2772 | 1307 | 336 | 1320 | 98 | 72 | 73.4694 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 91.5169 | 89.7281 | 93.3784 | 46.7817 | 1485 | 170 | 1382 | 98 | 58 | 59.1837 | |
| egarrison-hhga | SNP | * | map_l100_m2_e0 | het | 99.3648 | 98.9461 | 99.7870 | 65.4283 | 45910 | 489 | 45911 | 98 | 31 | 31.6327 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.2498 | 93.8518 | 98.7735 | 62.0410 | 7892 | 517 | 7892 | 98 | 83 | 84.6939 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.2447 | 97.1397 | 99.3753 | 55.6990 | 15588 | 459 | 15589 | 98 | 89 | 90.8163 | |
| ckim-dragen | SNP | * | * | homalt | 99.9725 | 99.9534 | 99.9917 | 17.1093 | 1179611 | 550 | 1179821 | 98 | 80 | 81.6327 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.2782 | 97.1365 | 99.4471 | 33.4959 | 10109 | 298 | 17626 | 98 | 90 | 91.8367 | |
| ciseli-custom | INDEL | C6_15 | HG002complexvar | * | 35.4067 | 50.0000 | 27.4074 | 91.9258 | 2 | 2 | 37 | 98 | 37 | 37.7551 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 85.2750 | 89.1170 | 81.7505 | 62.2628 | 434 | 53 | 439 | 98 | 30 | 30.6122 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 12.6208 | 7.7147 | 34.6667 | 87.4161 | 53 | 634 | 52 | 98 | 77 | 78.5714 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 41.4919 | 29.6496 | 69.0852 | 68.2046 | 220 | 522 | 219 | 98 | 82 | 83.6735 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 93.0016 | 90.9261 | 95.1741 | 68.8082 | 1944 | 194 | 1913 | 97 | 35 | 36.0825 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 92.2388 | 86.5886 | 98.6779 | 34.8864 | 7244 | 1122 | 7240 | 97 | 80 | 82.4742 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.2901 | 99.5113 | 97.0984 | 68.6486 | 3258 | 16 | 3246 | 97 | 94 | 96.9072 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.9553 | 99.4146 | 96.5382 | 63.5394 | 2717 | 16 | 2705 | 97 | 91 | 93.8144 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.0259 | 90.8384 | 97.4454 | 47.9934 | 3619 | 365 | 3700 | 97 | 76 | 78.3505 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 45.3035 | 36.1272 | 60.7287 | 71.8358 | 125 | 221 | 150 | 97 | 38 | 39.1753 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 16.9764 | 10.8209 | 39.3750 | 52.0958 | 58 | 478 | 63 | 97 | 77 | 79.3814 | |
| anovak-vg | SNP | * | map_l125_m2_e0 | homalt | 89.6412 | 81.6863 | 99.3125 | 67.9435 | 14193 | 3182 | 14013 | 97 | 81 | 83.5052 | |
| astatham-gatk | INDEL | * | HG002complexvar | homalt | 99.7747 | 99.9075 | 99.6422 | 57.3610 | 27002 | 25 | 27012 | 97 | 94 | 96.9072 | |
| asubramanian-gatk | INDEL | * | map_l100_m1_e0 | het | 89.5146 | 84.5190 | 95.1378 | 89.5888 | 1889 | 346 | 1898 | 97 | 13 | 13.4021 | |
| anovak-vg | INDEL | D1_5 | map_l125_m0_e0 | het | 80.1955 | 85.5072 | 75.5051 | 90.4922 | 295 | 50 | 299 | 97 | 38 | 39.1753 | |
| qzeng-custom | SNP | * | map_l125_m2_e0 | homalt | 83.6128 | 72.2475 | 99.2214 | 67.7362 | 12553 | 4822 | 12362 | 97 | 96 | 98.9691 | |
| ndellapenna-hhga | INDEL | I1_5 | HG002complexvar | homalt | 99.1510 | 99.0259 | 99.2764 | 48.8027 | 13317 | 131 | 13308 | 97 | 57 | 58.7629 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.4308 | 99.2074 | 99.6552 | 61.9169 | 28036 | 224 | 28038 | 97 | 74 | 76.2887 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 90.1316 | 95.9720 | 84.9612 | 56.9426 | 548 | 23 | 548 | 97 | 95 | 97.9381 | |
| mlin-fermikit | SNP | ti | segdup | homalt | 98.7142 | 98.7209 | 98.7075 | 85.2139 | 7409 | 96 | 7408 | 97 | 86 | 88.6598 | |
| mlin-fermikit | SNP | tv | map_l125_m2_e1 | het | 61.6520 | 44.9730 | 97.9955 | 67.0300 | 4746 | 5807 | 4742 | 97 | 1 | 1.0309 | |
| raldana-dualsentieon | SNP | ti | map_l250_m1_e0 | het | 97.3715 | 97.9784 | 96.7720 | 88.9838 | 2908 | 60 | 2908 | 97 | 2 | 2.0619 | |
| raldana-dualsentieon | INDEL | D16_PLUS | HG002compoundhet | * | 94.0691 | 92.4818 | 95.7118 | 34.3777 | 2165 | 176 | 2165 | 97 | 96 | 98.9691 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.8618 | 90.5873 | 97.3819 | 58.7738 | 3609 | 375 | 3608 | 97 | 92 | 94.8454 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 78.5568 | 68.4713 | 92.1266 | 57.1031 | 645 | 297 | 1135 | 97 | 92 | 94.8454 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 43.9004 | 28.4500 | 96.0776 | 48.1986 | 2041 | 5133 | 2376 | 97 | 95 | 97.9381 | |
| gduggal-bwaplat | SNP | * | map_l150_m2_e0 | * | 69.3373 | 53.2274 | 99.4313 | 91.0275 | 16954 | 14898 | 16958 | 97 | 30 | 30.9278 | |
| gduggal-bwaplat | SNP | * | map_l150_m2_e1 | het | 74.4402 | 59.5688 | 99.2072 | 92.2354 | 12130 | 8233 | 12138 | 97 | 27 | 27.8351 | |
| jpowers-varprowl | INDEL | D1_5 | map_l100_m2_e1 | * | 93.6537 | 92.4703 | 94.8677 | 84.4955 | 1793 | 146 | 1793 | 97 | 64 | 65.9794 | |
| jli-custom | SNP | ti | map_l150_m2_e1 | * | 99.2158 | 98.9046 | 99.5289 | 73.2251 | 20496 | 227 | 20494 | 97 | 36 | 37.1134 | |
| jpowers-varprowl | SNP | tv | map_siren | homalt | 99.3790 | 99.3213 | 99.4367 | 59.4375 | 17123 | 117 | 17123 | 97 | 72 | 74.2268 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.8166 | 98.1371 | 99.5056 | 55.0392 | 19492 | 370 | 19523 | 97 | 32 | 32.9897 | |
| 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 | |
| jmaeng-gatk | INDEL | D1_5 | map_siren | het | 97.5886 | 99.3412 | 95.8968 | 85.7195 | 2262 | 15 | 2267 | 97 | 5 | 5.1546 | |
| hfeng-pmm3 | SNP | ti | map_l125_m1_e0 | * | 99.5837 | 99.4989 | 99.6687 | 69.3283 | 29188 | 147 | 29184 | 97 | 16 | 16.4948 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 55.2682 | 73.5849 | 44.2529 | 77.4611 | 78 | 28 | 77 | 97 | 94 | 96.9072 | |
| ghariani-varprowl | SNP | ti | map_siren | homalt | 99.5932 | 99.4435 | 99.7434 | 52.5183 | 37705 | 211 | 37706 | 97 | 56 | 57.7320 | |
| gduggal-snapvard | INDEL | I6_15 | map_l100_m2_e0 | * | 60.8455 | 60.3448 | 61.3546 | 79.4431 | 70 | 46 | 154 | 97 | 79 | 81.4433 | |
| gduggal-snapvard | INDEL | I6_15 | map_l100_m2_e0 | het | 69.9557 | 88.5246 | 57.8261 | 79.7357 | 54 | 7 | 133 | 97 | 79 | 81.4433 | |
| gduggal-snapvard | INDEL | I6_15 | map_l100_m2_e1 | * | 60.9208 | 60.3448 | 61.5079 | 79.7590 | 70 | 46 | 155 | 97 | 79 | 81.4433 | |
| gduggal-snapvard | INDEL | I6_15 | map_l100_m2_e1 | het | 70.0891 | 88.5246 | 58.0087 | 80.0690 | 54 | 7 | 134 | 97 | 79 | 81.4433 | |
| egarrison-hhga | SNP | * | segdup | het | 99.4921 | 99.5438 | 99.4404 | 89.6178 | 17238 | 79 | 17238 | 97 | 4 | 4.1237 | |