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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
14451-14500 / 86044 show all | |||||||||||||||
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 95.7830 | 98.8722 | 92.8811 | 83.4809 | 1315 | 15 | 1109 | 85 | 72 | 84.7059 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 83.2099 | 96.3623 | 73.2167 | 70.3492 | 32026 | 1209 | 47861 | 17508 | 14830 | 84.7041 | |
| 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 | |
| ckim-vqsr | INDEL | I16_PLUS | * | * | 97.2630 | 96.1267 | 98.4265 | 70.8795 | 6130 | 247 | 6130 | 98 | 83 | 84.6939 | |
| qzeng-custom | SNP | * | map_l100_m0_e0 | * | 82.6366 | 72.0228 | 96.9194 | 83.3401 | 23653 | 9188 | 23407 | 744 | 630 | 84.6774 | |
| qzeng-custom | SNP | ti | map_l150_m1_e0 | het | 79.9066 | 68.7551 | 95.3758 | 89.6012 | 8505 | 3865 | 8477 | 411 | 348 | 84.6715 | |
| qzeng-custom | SNP | * | map_l125_m0_e0 | * | 78.3239 | 66.3606 | 95.5494 | 88.8093 | 12864 | 6521 | 12731 | 593 | 502 | 84.6543 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 85.3420 | 79.4704 | 92.1504 | 48.6116 | 2551 | 659 | 2524 | 215 | 182 | 84.6512 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.8694 | 96.4285 | 97.3143 | 66.9705 | 63017 | 2334 | 62795 | 1733 | 1467 | 84.6509 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.8694 | 96.4285 | 97.3143 | 66.9705 | 63017 | 2334 | 62795 | 1733 | 1467 | 84.6509 | |
| gduggal-snapplat | INDEL | D6_15 | HG002compoundhet | homalt | 5.2905 | 29.1667 | 2.9091 | 54.3189 | 7 | 17 | 8 | 267 | 226 | 84.6442 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 36.3779 | 31.5041 | 43.0357 | 63.8943 | 155 | 337 | 241 | 319 | 270 | 84.6395 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 52.0817 | 37.5305 | 85.0613 | 64.9709 | 4310 | 7174 | 4299 | 755 | 639 | 84.6358 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.2920 | 98.4666 | 96.1450 | 64.1784 | 12329 | 192 | 12171 | 488 | 413 | 84.6311 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.4328 | 98.7316 | 98.1358 | 49.9641 | 10275 | 132 | 10265 | 195 | 165 | 84.6154 | |
| hfeng-pmm1 | SNP | tv | HG002complexvar | homalt | 99.9763 | 99.9664 | 99.9863 | 22.9407 | 95079 | 32 | 95072 | 13 | 11 | 84.6154 | |
| jlack-gatk | SNP | ti | map_l100_m0_e0 | homalt | 98.9685 | 98.1219 | 99.8299 | 59.9927 | 7628 | 146 | 7628 | 13 | 11 | 84.6154 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.3930 | 99.3902 | 97.4155 | 59.5008 | 489 | 3 | 490 | 13 | 11 | 84.6154 | |
| jli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.9085 | 96.9156 | 98.9221 | 57.0053 | 1194 | 38 | 1193 | 13 | 11 | 84.6154 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.5423 | 89.2344 | 98.2872 | 66.4011 | 746 | 90 | 746 | 13 | 11 | 84.6154 | |
| gduggal-snapvard | INDEL | * | map_l125_m1_e0 | homalt | 92.3976 | 87.0219 | 98.4813 | 80.4522 | 637 | 95 | 843 | 13 | 11 | 84.6154 | |
| gduggal-snapvard | INDEL | * | map_l125_m2_e0 | homalt | 92.4285 | 87.0249 | 98.5475 | 81.2093 | 664 | 99 | 882 | 13 | 11 | 84.6154 | |
| gduggal-snapvard | INDEL | * | map_l125_m2_e1 | homalt | 92.3972 | 86.9509 | 98.5714 | 81.2719 | 673 | 101 | 897 | 13 | 11 | 84.6154 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 86.6360 | 76.8019 | 99.3583 | 29.3091 | 1950 | 589 | 2013 | 13 | 11 | 84.6154 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 88.4263 | 79.6804 | 99.3289 | 28.2061 | 1745 | 445 | 1924 | 13 | 11 | 84.6154 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 86.4817 | 76.5507 | 99.3735 | 30.6252 | 2024 | 620 | 2062 | 13 | 11 | 84.6154 | |
| raldana-dualsentieon | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5310 | 97.2348 | 99.8622 | 66.0735 | 9424 | 268 | 9424 | 13 | 11 | 84.6154 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 80.8511 | 80.2817 | 81.4286 | 43.5484 | 57 | 14 | 57 | 13 | 11 | 84.6154 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.2294 | 97.7556 | 96.7089 | 76.0751 | 392 | 9 | 382 | 13 | 11 | 84.6154 | |
| mlin-fermikit | INDEL | I1_5 | map_l150_m0_e0 | * | 50.5929 | 36.3636 | 83.1169 | 85.4717 | 64 | 112 | 64 | 13 | 11 | 84.6154 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 71.3699 | 57.0370 | 95.3237 | 59.0574 | 77 | 58 | 265 | 13 | 11 | 84.6154 | |
| gduggal-bwaplat | INDEL | D16_PLUS | * | homalt | 89.7870 | 82.0922 | 99.0734 | 63.7561 | 1389 | 303 | 1390 | 13 | 11 | 84.6154 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 58.6858 | 43.1579 | 91.6667 | 90.6222 | 287 | 378 | 286 | 26 | 22 | 84.6154 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 85.3906 | 75.6471 | 98.0153 | 59.9388 | 643 | 207 | 642 | 13 | 11 | 84.6154 | |
| gduggal-bwavard | SNP | tv | map_l100_m2_e0 | homalt | 98.7765 | 97.7209 | 99.8553 | 63.6981 | 9004 | 210 | 8971 | 13 | 11 | 84.6154 | |
| gduggal-bwavard | SNP | tv | map_l100_m2_e1 | homalt | 98.7497 | 97.6672 | 99.8565 | 63.7165 | 9085 | 217 | 9047 | 13 | 11 | 84.6154 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.4672 | 97.2859 | 99.6775 | 38.9821 | 20037 | 559 | 20088 | 65 | 55 | 84.6154 | |
| jmaeng-gatk | SNP | ti | HG002compoundhet | * | 99.3792 | 98.9129 | 99.8498 | 36.3432 | 17288 | 190 | 17288 | 26 | 22 | 84.6154 | |
| jmaeng-gatk | SNP | tv | HG002compoundhet | het | 99.2149 | 98.7160 | 99.7189 | 56.1374 | 4613 | 60 | 4611 | 13 | 11 | 84.6154 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.5269 | 91.7910 | 97.4308 | 60.3759 | 492 | 44 | 493 | 13 | 11 | 84.6154 | |
| ckim-isaac | INDEL | I16_PLUS | * | hetalt | 65.0682 | 48.5224 | 98.7366 | 42.1910 | 1018 | 1080 | 1016 | 13 | 11 | 84.6154 | |
| ckim-isaac | INDEL | I1_5 | HG002compoundhet | hetalt | 90.1858 | 82.6071 | 99.2955 | 37.7647 | 9233 | 1944 | 9162 | 65 | 55 | 84.6154 | |
| dgrover-gatk | SNP | ti | map_l100_m1_e0 | homalt | 99.7294 | 99.5323 | 99.9273 | 57.4153 | 17876 | 84 | 17876 | 13 | 11 | 84.6154 | |
| dgrover-gatk | SNP | ti | map_l100_m2_e0 | homalt | 99.7264 | 99.5248 | 99.9287 | 59.9046 | 18222 | 87 | 18222 | 13 | 11 | 84.6154 | |
| dgrover-gatk | SNP | ti | map_l100_m2_e1 | homalt | 99.7264 | 99.5242 | 99.9294 | 59.8793 | 18406 | 88 | 18406 | 13 | 11 | 84.6154 | |
| dgrover-gatk | SNP | tv | HG002complexvar | homalt | 99.9637 | 99.9411 | 99.9863 | 22.7977 | 95055 | 56 | 95040 | 13 | 11 | 84.6154 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 96.9267 | 100.0000 | 94.0367 | 91.2309 | 205 | 0 | 205 | 13 | 11 | 84.6154 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 96.9267 | 100.0000 | 94.0367 | 91.2309 | 205 | 0 | 205 | 13 | 11 | 84.6154 | |
| eyeh-varpipe | INDEL | * | func_cds | * | 95.4669 | 93.9326 | 97.0522 | 79.5644 | 418 | 27 | 428 | 13 | 11 | 84.6154 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.3574 | 99.5074 | 95.2984 | 84.1819 | 606 | 3 | 527 | 26 | 22 | 84.6154 | |