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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
40701-40750 / 86044 show all | |||||||||||||||
| asubramanian-gatk | INDEL | I1_5 | map_l150_m0_e0 | het | 87.2549 | 83.9623 | 90.8163 | 95.3356 | 89 | 17 | 89 | 9 | 0 | 0.0000 | |
| gduggal-snapvard | SNP | * | map_l125_m1_e0 | * | 93.5846 | 96.5275 | 90.8158 | 77.9328 | 43753 | 1574 | 43182 | 4367 | 333 | 7.6254 | |
| ltrigg-rtg1 | INDEL | C1_5 | * | het | 89.8401 | 88.8889 | 90.8120 | 96.3931 | 8 | 1 | 425 | 43 | 1 | 2.3256 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 17.8608 | 9.9044 | 90.8088 | 60.0587 | 373 | 3393 | 247 | 25 | 25 | 100.0000 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 17.8608 | 9.9044 | 90.8088 | 60.0587 | 373 | 3393 | 247 | 25 | 25 | 100.0000 | |
| gduggal-snapvard | SNP | ti | map_l100_m1_e0 | het | 93.5196 | 96.3997 | 90.8067 | 76.8858 | 28864 | 1078 | 28615 | 2897 | 247 | 8.5261 | |
| ckim-gatk | INDEL | D1_5 | map_l125_m1_e0 | het | 94.7425 | 99.0358 | 90.8060 | 91.1611 | 719 | 7 | 721 | 73 | 4 | 5.4795 | |
| hfeng-pmm3 | INDEL | D16_PLUS | map_l100_m1_e0 | * | 90.8046 | 90.8046 | 90.8046 | 92.7980 | 79 | 8 | 79 | 8 | 2 | 25.0000 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 85.4239 | 80.6452 | 90.8046 | 75.2137 | 50 | 12 | 158 | 16 | 16 | 100.0000 | |
| gduggal-bwavard | INDEL | * | HG002complexvar | * | 90.6853 | 90.5690 | 90.8018 | 55.4471 | 69682 | 7256 | 68628 | 6952 | 5563 | 80.0201 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 86.2959 | 82.2171 | 90.8006 | 44.5699 | 3204 | 693 | 7531 | 763 | 673 | 88.2045 | |
| jli-custom | INDEL | D6_15 | HG002compoundhet | het | 93.6150 | 96.6121 | 90.7982 | 65.4935 | 827 | 29 | 819 | 83 | 81 | 97.5904 | |
| gduggal-bwavard | INDEL | I1_5 | map_l125_m2_e1 | het | 94.3638 | 98.2283 | 90.7919 | 91.5103 | 499 | 9 | 493 | 50 | 22 | 44.0000 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.9504 | 99.5147 | 90.7864 | 82.3867 | 3896 | 19 | 3902 | 396 | 320 | 80.8081 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 88.0678 | 85.5096 | 90.7838 | 68.5024 | 1074 | 182 | 1054 | 107 | 48 | 44.8598 | |
| mlin-fermikit | INDEL | I6_15 | HG002complexvar | het | 91.0577 | 91.3376 | 90.7795 | 57.5294 | 2151 | 204 | 2166 | 220 | 217 | 98.6364 | |
| gduggal-bwavard | SNP | * | map_l125_m2_e1 | het | 94.2043 | 97.9082 | 90.7704 | 83.1773 | 29020 | 620 | 28678 | 2916 | 165 | 5.6584 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 89.9308 | 89.1078 | 90.7692 | 60.4401 | 769 | 94 | 767 | 78 | 76 | 97.4359 | |
| gduggal-snapfb | INDEL | D1_5 | map_l250_m2_e1 | het | 93.6508 | 96.7213 | 90.7692 | 93.7137 | 118 | 4 | 118 | 12 | 1 | 8.3333 | |
| gduggal-snapfb | INDEL | I1_5 | func_cds | het | 93.5987 | 96.6102 | 90.7692 | 41.4414 | 57 | 2 | 59 | 6 | 1 | 16.6667 | |
| ckim-vqsr | INDEL | D6_15 | map_l100_m0_e0 | het | 94.4000 | 98.3333 | 90.7692 | 93.0851 | 59 | 1 | 59 | 6 | 1 | 16.6667 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 86.9792 | 83.5000 | 90.7609 | 61.7464 | 167 | 33 | 167 | 17 | 13 | 76.4706 | |
| anovak-vg | INDEL | D1_5 | HG002complexvar | homalt | 92.9611 | 95.2727 | 90.7590 | 57.9711 | 10097 | 501 | 10224 | 1041 | 840 | 80.6916 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 80.6824 | 72.6236 | 90.7531 | 35.9976 | 955 | 360 | 952 | 97 | 93 | 95.8763 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 27.1199 | 15.9420 | 90.7489 | 71.4824 | 143 | 754 | 206 | 21 | 19 | 90.4762 | |
| gduggal-bwaplat | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 49.0051 | 33.5664 | 90.7407 | 98.6432 | 48 | 95 | 49 | 5 | 3 | 60.0000 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 88.3609 | 86.1027 | 90.7407 | 70.8221 | 570 | 92 | 686 | 70 | 40 | 57.1429 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 89.1839 | 87.6797 | 90.7407 | 59.6010 | 427 | 60 | 441 | 45 | 26 | 57.7778 | |
| jlack-gatk | INDEL | D6_15 | map_l100_m1_e0 | * | 92.8030 | 94.9612 | 90.7407 | 88.2660 | 245 | 13 | 245 | 25 | 3 | 12.0000 | |
| hfeng-pmm3 | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | het | 81.6667 | 74.2424 | 90.7407 | 94.0463 | 49 | 17 | 49 | 5 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | * | map_l250_m0_e0 | het | 91.5888 | 92.4528 | 90.7407 | 96.9849 | 49 | 4 | 49 | 5 | 1 | 20.0000 | |
| mlin-fermikit | SNP | * | map_l100_m1_e0 | * | 72.2095 | 59.9657 | 90.7360 | 51.7425 | 43417 | 28986 | 43409 | 4432 | 3924 | 88.5379 | |
| ciseli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 94.8802 | 99.4227 | 90.7347 | 62.0390 | 2239 | 13 | 2223 | 227 | 39 | 17.1806 | |
| qzeng-custom | INDEL | * | map_siren | het | 88.2436 | 85.8917 | 90.7279 | 86.0479 | 3872 | 636 | 4325 | 442 | 93 | 21.0407 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 95.1351 | 100.0000 | 90.7216 | 63.3962 | 68 | 0 | 88 | 9 | 4 | 44.4444 | |
| qzeng-custom | INDEL | I16_PLUS | HG002complexvar | het | 88.3834 | 86.1654 | 90.7186 | 58.7909 | 573 | 92 | 606 | 62 | 11 | 17.7419 | |
| qzeng-custom | INDEL | * | map_l150_m0_e0 | het | 80.0048 | 71.5543 | 90.7186 | 97.0277 | 244 | 97 | 303 | 31 | 16 | 51.6129 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 94.1563 | 97.8654 | 90.7180 | 83.3187 | 596 | 13 | 518 | 53 | 40 | 75.4717 | |
| qzeng-custom | INDEL | I1_5 | HG002compoundhet | * | 82.4804 | 75.6151 | 90.7168 | 64.6037 | 9343 | 3013 | 9391 | 961 | 822 | 85.5359 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 92.9003 | 95.1929 | 90.7155 | 79.9240 | 16159 | 816 | 16190 | 1657 | 193 | 11.6476 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 92.9003 | 95.1929 | 90.7155 | 79.9240 | 16159 | 816 | 16190 | 1657 | 193 | 11.6476 | |
| cchapple-custom | INDEL | C6_15 | * | het | 95.1311 | 100.0000 | 90.7143 | 93.8570 | 7 | 0 | 254 | 26 | 10 | 38.4615 | |
| ghariani-varprowl | INDEL | I1_5 | segdup | * | 91.1523 | 91.5958 | 90.7129 | 95.2994 | 970 | 89 | 967 | 99 | 67 | 67.6768 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 94.6615 | 98.9726 | 90.7104 | 82.2631 | 867 | 9 | 664 | 68 | 63 | 92.6471 | |
| gduggal-bwavard | SNP | * | map_l125_m2_e0 | het | 94.1644 | 97.8921 | 90.7102 | 83.1354 | 28700 | 618 | 28366 | 2905 | 164 | 5.6454 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 85.8273 | 81.4433 | 90.7101 | 41.4412 | 2844 | 648 | 7128 | 730 | 664 | 90.9589 | |
| jlack-gatk | SNP | tv | map_l150_m2_e1 | * | 94.5415 | 98.7220 | 90.7006 | 84.3649 | 11355 | 147 | 11353 | 1164 | 68 | 5.8419 | |
| gduggal-snapfb | INDEL | I6_15 | map_l125_m1_e0 | * | 81.2500 | 73.5849 | 90.6977 | 82.0084 | 39 | 14 | 39 | 4 | 3 | 75.0000 | |
| gduggal-snapfb | INDEL | I6_15 | map_l125_m2_e0 | * | 81.2500 | 73.5849 | 90.6977 | 84.4765 | 39 | 14 | 39 | 4 | 3 | 75.0000 | |
| gduggal-snapfb | INDEL | I6_15 | map_l125_m2_e1 | * | 81.2500 | 73.5849 | 90.6977 | 85.1724 | 39 | 14 | 39 | 4 | 3 | 75.0000 | |