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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
38851-38900 / 86044 show all | |||||||||||||||
| mlin-fermikit | SNP | * | map_l125_m1_e0 | homalt | 65.3755 | 57.2079 | 76.2637 | 52.9793 | 9671 | 7234 | 9671 | 3010 | 2851 | 94.7176 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 48.6351 | 57.2200 | 42.2902 | 47.0270 | 424 | 317 | 746 | 1018 | 780 | 76.6208 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 61.3754 | 57.2372 | 66.1586 | 39.2942 | 14046 | 10494 | 14021 | 7172 | 7085 | 98.7869 | |
| mlin-fermikit | INDEL | I1_5 | map_l100_m2_e0 | het | 71.6654 | 57.2509 | 95.7806 | 78.7349 | 454 | 339 | 454 | 20 | 12 | 60.0000 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 63.5631 | 57.2581 | 71.4286 | 99.8537 | 71 | 53 | 65 | 26 | 10 | 38.4615 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 71.8309 | 57.2785 | 96.2963 | 83.2149 | 181 | 135 | 182 | 7 | 5 | 71.4286 | |
| gduggal-snapfb | INDEL | I6_15 | HG002compoundhet | * | 66.9443 | 57.2812 | 80.5291 | 25.2164 | 5027 | 3749 | 5844 | 1413 | 1393 | 98.5846 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 71.0987 | 57.2816 | 93.7008 | 58.7662 | 118 | 88 | 119 | 8 | 2 | 25.0000 | |
| gduggal-bwaplat | INDEL | D6_15 | map_l100_m0_e0 | * | 72.3926 | 57.2816 | 98.3333 | 96.0186 | 59 | 44 | 59 | 1 | 0 | 0.0000 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 71.8529 | 57.2932 | 96.3338 | 35.0041 | 762 | 568 | 762 | 29 | 27 | 93.1034 | |
| jmaeng-gatk | SNP | * | map_l150_m2_e1 | homalt | 72.8475 | 57.3011 | 99.9705 | 80.8330 | 6777 | 5050 | 6777 | 2 | 2 | 100.0000 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 64.6284 | 57.3034 | 74.1007 | 75.4850 | 102 | 76 | 103 | 36 | 35 | 97.2222 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 60.5878 | 57.3058 | 64.2686 | 55.8452 | 6581 | 4903 | 7763 | 4316 | 3401 | 78.7998 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 42.3423 | 57.3171 | 33.5714 | 78.0220 | 47 | 35 | 47 | 93 | 26 | 27.9570 | |
| mlin-fermikit | SNP | tv | map_l125_m1_e0 | homalt | 63.9810 | 57.3208 | 72.3922 | 52.9173 | 3359 | 2501 | 3359 | 1281 | 1204 | 93.9891 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 67.8720 | 57.3310 | 83.1622 | 50.3568 | 2002 | 1490 | 1215 | 246 | 238 | 96.7480 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 69.8922 | 57.3374 | 89.4866 | 50.3641 | 1516 | 1128 | 366 | 43 | 39 | 90.6977 | |
| mlin-fermikit | SNP | ti | map_l100_m2_e1 | het | 72.5397 | 57.3547 | 98.6610 | 56.4877 | 17757 | 13203 | 17757 | 241 | 9 | 3.7344 | |
| ciseli-custom | INDEL | I1_5 | HG002compoundhet | het | 44.8253 | 57.3616 | 36.7858 | 80.5882 | 487 | 362 | 998 | 1715 | 1422 | 82.9155 | |
| gduggal-bwaplat | SNP | tv | map_l150_m2_e0 | het | 72.7336 | 57.3635 | 99.3551 | 93.0443 | 4160 | 3092 | 4160 | 27 | 5 | 18.5185 | |
| ckim-isaac | INDEL | * | map_l100_m0_e0 | homalt | 72.6368 | 57.3674 | 98.9831 | 75.1684 | 292 | 217 | 292 | 3 | 1 | 33.3333 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 72.5735 | 57.3752 | 98.7253 | 40.9262 | 1517 | 1127 | 1549 | 20 | 20 | 100.0000 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 72.1649 | 57.3770 | 97.2222 | 62.8866 | 35 | 26 | 35 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 72.9167 | 57.3770 | 100.0000 | 85.5967 | 35 | 26 | 35 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | D1_5 | map_l125_m2_e0 | homalt | 72.9494 | 57.4176 | 100.0000 | 91.2000 | 209 | 155 | 209 | 0 | 0 | ||
| ckim-isaac | INDEL | D1_5 | map_l125_m2_e0 | homalt | 72.8223 | 57.4176 | 99.5238 | 81.1321 | 209 | 155 | 209 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 72.8203 | 57.4281 | 99.4845 | 34.4595 | 719 | 533 | 193 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 68.3544 | 57.4468 | 84.3750 | 66.6667 | 27 | 20 | 27 | 5 | 3 | 60.0000 | |
| qzeng-custom | INDEL | I16_PLUS | HG002compoundhet | het | 64.8870 | 57.4468 | 74.5413 | 60.7207 | 27 | 20 | 325 | 111 | 71 | 63.9640 | |
| mlin-fermikit | INDEL | I16_PLUS | HG002compoundhet | het | 6.2171 | 57.4468 | 3.2864 | 65.0533 | 27 | 20 | 14 | 412 | 412 | 100.0000 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 59.8171 | 57.4468 | 62.3913 | 40.7216 | 108 | 80 | 287 | 173 | 145 | 83.8150 | |
| ckim-gatk | SNP | * | map_l150_m0_e0 | * | 72.2501 | 57.4634 | 97.2832 | 92.5200 | 6914 | 5118 | 6911 | 193 | 26 | 13.4715 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 70.2459 | 57.4713 | 90.3226 | 99.9104 | 50 | 37 | 56 | 6 | 3 | 50.0000 | |
| gduggal-bwavard | INDEL | D16_PLUS | map_l100_m1_e0 | * | 54.0541 | 57.4713 | 51.0204 | 92.8363 | 50 | 37 | 50 | 48 | 21 | 43.7500 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m0_e0 | * | 68.2636 | 57.4739 | 84.0407 | 76.2404 | 496 | 367 | 495 | 94 | 78 | 82.9787 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 63.0461 | 57.4841 | 69.7998 | 69.3027 | 722 | 534 | 802 | 347 | 171 | 49.2795 | |
| ciseli-custom | SNP | * | map_l250_m2_e0 | het | 62.7486 | 57.4894 | 69.0669 | 93.5182 | 2986 | 2208 | 2983 | 1336 | 41 | 3.0689 | |
| gduggal-bwaplat | SNP | tv | map_l100_m1_e0 | homalt | 73.0094 | 57.4920 | 100.0000 | 72.7511 | 5199 | 3844 | 5198 | 0 | 0 | ||
| qzeng-custom | SNP | ti | map_l250_m1_e0 | homalt | 72.8401 | 57.4984 | 99.3478 | 88.5158 | 924 | 683 | 914 | 6 | 6 | 100.0000 | |
| gduggal-bwaplat | INDEL | * | map_l125_m1_e0 | hetalt | 73.0159 | 57.5000 | 100.0000 | 97.2121 | 23 | 17 | 23 | 0 | 0 | ||
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 70.0566 | 57.5000 | 89.6296 | 82.8897 | 115 | 85 | 121 | 14 | 5 | 35.7143 | |
| jmaeng-gatk | SNP | * | map_l150_m0_e0 | * | 72.2268 | 57.5050 | 97.0803 | 92.6384 | 6919 | 5113 | 6916 | 208 | 23 | 11.0577 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 60.2687 | 57.5149 | 63.2995 | 49.8576 | 2120 | 1566 | 2118 | 1228 | 856 | 69.7068 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 68.5647 | 57.5184 | 84.8624 | 93.9078 | 547 | 404 | 555 | 99 | 45 | 45.4545 | |
| ckim-gatk | SNP | ti | map_l150_m2_e0 | homalt | 73.0167 | 57.5236 | 99.9316 | 81.2297 | 4381 | 3235 | 4381 | 3 | 2 | 66.6667 | |
| gduggal-bwaplat | INDEL | D1_5 | map_l125_m2_e1 | homalt | 73.0375 | 57.5269 | 100.0000 | 91.1825 | 214 | 158 | 214 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 72.8368 | 57.5419 | 99.2063 | 28.0000 | 103 | 76 | 125 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | I1_5 | map_l250_m1_e0 | * | 73.0539 | 57.5472 | 100.0000 | 96.9176 | 61 | 45 | 61 | 0 | 0 | ||
| ckim-isaac | SNP | * | map_l100_m1_e0 | homalt | 73.0435 | 57.5492 | 99.9550 | 54.3192 | 15540 | 11463 | 15540 | 7 | 7 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | map_l100_m0_e0 | * | 72.8908 | 57.5582 | 99.3581 | 86.0136 | 12531 | 9240 | 12537 | 81 | 26 | 32.0988 | |