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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
2251-2300 / 86044 show all | |||||||||||||||
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 81.2086 | 91.0256 | 73.3029 | 53.9573 | 4047 | 399 | 4017 | 1463 | 1454 | 99.3848 | |
| jlack-gatk | SNP | tv | map_l125_m2_e0 | het | 92.9966 | 99.0806 | 87.6165 | 84.4986 | 10346 | 96 | 10344 | 1462 | 81 | 5.5404 | |
| ckim-dragen | SNP | ti | map_siren | het | 98.6081 | 99.5319 | 97.7013 | 60.9808 | 62090 | 292 | 62097 | 1461 | 137 | 9.3771 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 41.3724 | 88.2160 | 27.0230 | 51.3251 | 539 | 72 | 541 | 1461 | 1457 | 99.7262 | |
| anovak-vg | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 59.0705 | 52.5583 | 67.4247 | 65.2810 | 1397 | 1261 | 3024 | 1461 | 1247 | 85.3525 | |
| jlack-gatk | SNP | tv | map_l125_m1_e0 | * | 95.0729 | 98.8636 | 91.5621 | 79.9369 | 15834 | 182 | 15832 | 1459 | 89 | 6.1001 | |
| gduggal-snapfb | SNP | * | map_l125_m2_e0 | * | 96.9292 | 96.9758 | 96.8828 | 74.5886 | 45310 | 1413 | 45314 | 1458 | 623 | 42.7298 | |
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 19.2653 | 18.2294 | 20.4260 | 59.9344 | 383 | 1718 | 374 | 1457 | 1446 | 99.2450 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 84.4065 | 96.1747 | 75.2044 | 56.2444 | 3721 | 148 | 4416 | 1456 | 1419 | 97.4588 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 44.2793 | 38.8052 | 51.5516 | 63.0411 | 1546 | 2438 | 1545 | 1452 | 1385 | 95.3857 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 81.5998 | 93.5118 | 72.3797 | 87.9363 | 3877 | 269 | 3805 | 1452 | 65 | 4.4766 | |
| gduggal-bwavard | SNP | ti | map_l100_m0_e0 | * | 95.3330 | 97.2027 | 93.5339 | 77.3132 | 21162 | 609 | 20989 | 1451 | 95 | 6.5472 | |
| mlin-fermikit | INDEL | I6_15 | HG002compoundhet | het | 11.9006 | 62.5000 | 6.5764 | 49.1309 | 130 | 78 | 102 | 1449 | 1446 | 99.7930 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 40.2175 | 43.3884 | 37.4784 | 42.9557 | 420 | 548 | 868 | 1448 | 1173 | 81.0083 | |
| gduggal-snapplat | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 84.8609 | 77.5453 | 93.7004 | 78.4378 | 21463 | 6215 | 21508 | 1446 | 158 | 10.9267 | |
| jlack-gatk | SNP | tv | map_l125_m1_e0 | het | 92.8605 | 99.0519 | 87.3976 | 83.4310 | 10030 | 96 | 10028 | 1446 | 80 | 5.5325 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 89.3383 | 88.9709 | 89.7087 | 51.9572 | 7470 | 926 | 12596 | 1445 | 343 | 23.7370 | |
| mlin-fermikit | SNP | * | map_l125_m0_e0 | homalt | 56.5095 | 47.8546 | 68.9863 | 54.6729 | 3212 | 3500 | 3212 | 1444 | 1335 | 92.4515 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 13.3646 | 83.0645 | 7.2669 | 75.3956 | 103 | 21 | 113 | 1442 | 13 | 0.9015 | |
| ghariani-varprowl | INDEL | I1_5 | * | homalt | 94.4302 | 91.5834 | 97.4597 | 39.6857 | 55342 | 5086 | 55284 | 1441 | 928 | 64.3997 | |
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 28.8874 | 67.7551 | 18.3569 | 52.9208 | 332 | 158 | 324 | 1441 | 1432 | 99.3754 | |
| gduggal-snapvard | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 54.3265 | 100.0000 | 37.2933 | 91.2179 | 3 | 0 | 857 | 1441 | 188 | 13.0465 | |
| jlack-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.3660 | 98.2626 | 98.4696 | 72.6251 | 92808 | 1641 | 92717 | 1441 | 1058 | 73.4212 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.1122 | 95.6040 | 96.6259 | 60.2914 | 41430 | 1905 | 41238 | 1440 | 1303 | 90.4861 | |
| gduggal-snapplat | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 79.9070 | 76.3413 | 83.8220 | 85.1082 | 7399 | 2293 | 7461 | 1440 | 187 | 12.9861 | |
| ckim-dragen | SNP | * | map_l100_m2_e1 | het | 98.1019 | 99.2281 | 97.0009 | 73.9476 | 46536 | 362 | 46542 | 1439 | 120 | 8.3391 | |
| gduggal-bwavard | SNP | ti | map_l100_m0_e0 | het | 93.7781 | 97.4183 | 90.4002 | 80.9729 | 13622 | 361 | 13532 | 1437 | 84 | 5.8455 | |
| gduggal-snapfb | SNP | * | map_l125_m1_e0 | * | 96.8640 | 96.8959 | 96.8321 | 72.7854 | 43920 | 1407 | 43924 | 1437 | 620 | 43.1454 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 82.0492 | 96.8053 | 71.1966 | 41.3611 | 2212 | 73 | 3552 | 1437 | 1234 | 85.8733 | |
| gduggal-snapfb | SNP | ti | map_siren | het | 98.2591 | 98.8009 | 97.7232 | 58.6413 | 61634 | 748 | 61636 | 1436 | 494 | 34.4011 | |
| anovak-vg | INDEL | D1_5 | HG002complexvar | het | 92.0015 | 90.8693 | 93.1622 | 52.9821 | 18869 | 1896 | 19565 | 1436 | 834 | 58.0780 | |
| asubramanian-gatk | INDEL | * | * | het | 98.9698 | 98.6849 | 99.2562 | 61.7813 | 191580 | 2553 | 191238 | 1433 | 589 | 41.1026 | |
| ckim-isaac | INDEL | D1_5 | * | het | 97.9869 | 97.6340 | 98.3423 | 46.0249 | 85502 | 2072 | 85013 | 1433 | 986 | 68.8067 | |
| gduggal-bwavard | SNP | ti | map_l150_m2_e1 | * | 95.4042 | 97.5776 | 93.3256 | 83.0965 | 20221 | 502 | 20037 | 1433 | 94 | 6.5597 | |
| ciseli-custom | SNP | * | map_l150_m0_e0 | het | 70.4472 | 64.1940 | 78.0503 | 88.1313 | 5097 | 2843 | 5092 | 1432 | 47 | 3.2821 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 79.3723 | 90.3851 | 70.7516 | 51.9765 | 3497 | 372 | 3464 | 1432 | 1427 | 99.6508 | |
| ndellapenna-hhga | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 81.6855 | 91.2376 | 73.9439 | 67.5049 | 3686 | 354 | 4061 | 1431 | 1308 | 91.4046 | |
| ckim-dragen | SNP | * | map_l100_m2_e0 | het | 98.0933 | 99.2263 | 96.9859 | 73.8971 | 46040 | 359 | 46046 | 1431 | 119 | 8.3159 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 60.6700 | 53.9166 | 69.3576 | 54.0626 | 3063 | 2618 | 3239 | 1431 | 1089 | 76.1006 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 20.0419 | 16.9448 | 24.5243 | 50.5230 | 467 | 2289 | 464 | 1428 | 1427 | 99.9300 | |
| ghariani-varprowl | INDEL | D16_PLUS | HG002compoundhet | * | 18.0085 | 15.8906 | 20.7778 | 37.7809 | 372 | 1969 | 374 | 1426 | 1417 | 99.3689 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 75.3471 | 93.5728 | 63.0638 | 89.0931 | 2475 | 170 | 2433 | 1425 | 52 | 3.6491 | |
| gduggal-bwavard | SNP | ti | map_l150_m2_e0 | * | 95.3841 | 97.5624 | 93.3010 | 83.0334 | 20012 | 500 | 19833 | 1424 | 93 | 6.5309 | |
| gduggal-bwavard | SNP | ti | map_l150_m2_e1 | het | 93.6574 | 97.7641 | 89.8818 | 85.8419 | 12724 | 291 | 12623 | 1421 | 85 | 5.9817 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 93.5454 | 91.9051 | 95.2453 | 77.4805 | 28622 | 2521 | 28425 | 1419 | 235 | 16.5610 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 93.5454 | 91.9051 | 95.2453 | 77.4805 | 28622 | 2521 | 28425 | 1419 | 235 | 16.5610 | |
| gduggal-snapvard | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 49.3757 | 100.0000 | 32.7807 | 90.9114 | 3 | 0 | 692 | 1419 | 174 | 12.2622 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.1638 | 96.5250 | 97.8111 | 70.9066 | 62192 | 2239 | 63408 | 1419 | 1076 | 75.8280 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 52.6451 | 49.8736 | 55.7428 | 73.7700 | 1776 | 1785 | 1786 | 1418 | 1371 | 96.6855 | |
| ckim-dragen | SNP | * | map_l100_m1_e0 | * | 98.6742 | 99.2901 | 98.0660 | 67.7530 | 71889 | 514 | 71900 | 1418 | 151 | 10.6488 | |