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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
59951-60000 / 86044 show all | |||||||||||||||
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.2810 | 93.7940 | 96.8159 | 46.5107 | 2796 | 185 | 3740 | 123 | 114 | 92.6829 | |
| bgallagher-sentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 100.0000 | 100.0000 | 100.0000 | 46.5087 | 858 | 0 | 858 | 0 | 0 | ||
| jlack-gatk | INDEL | D6_15 | HG002compoundhet | homalt | 19.5122 | 100.0000 | 10.8108 | 46.5060 | 24 | 0 | 24 | 198 | 197 | 99.4949 | |
| asubramanian-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.9417 | 99.8834 | 100.0000 | 46.5044 | 857 | 1 | 857 | 0 | 0 | ||
| astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.9417 | 99.8834 | 100.0000 | 46.5044 | 857 | 1 | 857 | 0 | 0 | ||
| qzeng-custom | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.0581 | 99.5974 | 96.5657 | 46.5037 | 7422 | 30 | 7395 | 263 | 9 | 3.4221 | |
| cchapple-custom | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.4328 | 99.7924 | 99.0758 | 46.4998 | 6730 | 14 | 6754 | 63 | 6 | 9.5238 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 98.1325 | 96.5309 | 99.7881 | 46.4918 | 3673 | 132 | 3767 | 8 | 8 | 100.0000 | |
| gduggal-snapplat | INDEL | I6_15 | * | hetalt | 52.6793 | 36.6390 | 93.7008 | 46.4917 | 3133 | 5418 | 3094 | 208 | 167 | 80.2885 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 43.7158 | 29.2554 | 86.4426 | 46.4806 | 1497 | 3620 | 1492 | 234 | 208 | 88.8889 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 91.0906 | 96.0483 | 86.6196 | 46.4616 | 2625 | 108 | 7477 | 1155 | 540 | 46.7532 | |
| jli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8670 | 99.8227 | 99.9113 | 46.4608 | 1126 | 2 | 1126 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.5204 | 99.2823 | 99.7596 | 46.4607 | 415 | 3 | 415 | 1 | 1 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.9685 | 94.3268 | 99.7624 | 46.4589 | 2494 | 150 | 2519 | 6 | 5 | 83.3333 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 100.0000 | 100.0000 | 100.0000 | 46.4467 | 211 | 0 | 211 | 0 | 0 | ||
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 93.7961 | 88.8038 | 99.3832 | 46.4455 | 7424 | 936 | 7412 | 46 | 33 | 71.7391 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 93.7961 | 88.8038 | 99.3832 | 46.4455 | 7424 | 936 | 7412 | 46 | 33 | 71.7391 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 91.0394 | 84.1060 | 99.2188 | 46.4435 | 127 | 24 | 127 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 82.6406 | 75.4390 | 91.3622 | 46.4432 | 2964 | 965 | 3226 | 305 | 294 | 96.3934 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 97.2152 | 100.0000 | 94.5813 | 46.4380 | 192 | 0 | 192 | 11 | 10 | 90.9091 | |
| gduggal-bwafb | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7130 | 99.7766 | 99.6495 | 46.4322 | 6254 | 14 | 6254 | 22 | 9 | 40.9091 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.6431 | 99.2888 | 100.0000 | 46.4313 | 698 | 5 | 698 | 0 | 0 | ||
| anovak-vg | INDEL | D6_15 | func_cds | het | 81.3559 | 82.7586 | 80.0000 | 46.4286 | 24 | 5 | 24 | 6 | 5 | 83.3333 | |
| qzeng-custom | INDEL | I6_15 | tech_badpromoters | * | 85.6287 | 84.6154 | 86.6667 | 46.4286 | 11 | 2 | 13 | 2 | 2 | 100.0000 | |
| hfeng-pmm2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.8634 | 99.7271 | 100.0000 | 46.4273 | 1462 | 4 | 1462 | 0 | 0 | ||
| jpowers-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 24.0700 | 40.7407 | 17.0807 | 46.4226 | 55 | 80 | 55 | 267 | 265 | 99.2509 | |
| eyeh-varpipe | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.3412 | 97.9740 | 96.7165 | 46.4205 | 3385 | 70 | 2975 | 101 | 32 | 31.6832 | |
| asubramanian-gatk | SNP | ti | * | hetalt | 95.6522 | 94.5017 | 96.8310 | 46.4151 | 550 | 32 | 550 | 18 | 1 | 5.5556 | |
| ckim-dragen | SNP | * | HG002compoundhet | het | 99.7322 | 99.6967 | 99.7677 | 46.4046 | 14135 | 43 | 14173 | 33 | 8 | 24.2424 | |
| ckim-dragen | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.9417 | 99.8834 | 100.0000 | 46.3975 | 857 | 1 | 863 | 0 | 0 | ||
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 86.1593 | 93.2312 | 80.0845 | 46.3972 | 5661 | 411 | 9663 | 2403 | 2342 | 97.4615 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1747 | 97.0673 | 99.3076 | 46.3948 | 10757 | 325 | 10757 | 75 | 72 | 96.0000 | |
| anovak-vg | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 67.8590 | 93.2584 | 53.3333 | 46.3895 | 249 | 18 | 392 | 343 | 331 | 96.5015 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.8028 | 97.6785 | 97.9275 | 46.3889 | 7279 | 173 | 7182 | 152 | 45 | 29.6053 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.4859 | 99.1534 | 99.8206 | 46.3856 | 6676 | 57 | 6678 | 12 | 5 | 41.6667 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 63.5479 | 97.2152 | 47.2013 | 46.3823 | 6493 | 186 | 6527 | 7301 | 7199 | 98.6029 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 98.2763 | 96.9365 | 99.6537 | 46.3792 | 2563 | 81 | 2590 | 9 | 8 | 88.8889 | |
| eyeh-varpipe | INDEL | * | tech_badpromoters | het | 91.9609 | 87.1795 | 97.2973 | 46.3768 | 34 | 5 | 36 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | SNP | * | tech_badpromoters | het | 98.0132 | 96.1039 | 100.0000 | 46.3768 | 74 | 3 | 74 | 0 | 0 | ||
| ciseli-custom | INDEL | I6_15 | * | * | 35.4599 | 24.6948 | 62.8636 | 46.3768 | 6130 | 18693 | 6094 | 3600 | 3400 | 94.4444 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1240 | 97.6833 | 98.5687 | 46.3695 | 17836 | 423 | 17837 | 259 | 256 | 98.8417 | |
| hfeng-pmm1 | SNP | * | tech_badpromoters | * | 99.3590 | 98.7261 | 100.0000 | 46.3668 | 155 | 2 | 155 | 0 | 0 | ||
| gduggal-bwavard | INDEL | * | func_cds | * | 92.3991 | 93.2584 | 91.5556 | 46.3647 | 415 | 30 | 412 | 38 | 24 | 63.1579 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 91.3934 | 84.1509 | 100.0000 | 46.3584 | 446 | 84 | 464 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.4778 | 99.2346 | 99.7223 | 46.3498 | 3630 | 28 | 3591 | 10 | 1 | 10.0000 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 77.2779 | 63.3540 | 99.0460 | 46.3471 | 1122 | 649 | 1142 | 11 | 11 | 100.0000 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 61.5928 | 47.2536 | 88.4257 | 46.3421 | 1798 | 2007 | 1803 | 236 | 207 | 87.7119 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 91.8091 | 85.5307 | 99.0822 | 46.3398 | 2329 | 394 | 2375 | 22 | 22 | 100.0000 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 82.5318 | 70.7702 | 98.9822 | 46.3359 | 1167 | 482 | 1167 | 12 | 11 | 91.6667 | |
| qzeng-custom | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6888 | 99.5692 | 99.8086 | 46.3323 | 6241 | 27 | 6258 | 12 | 2 | 16.6667 | |