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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
4151-4200 / 86044 show all | |||||||||||||||
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 70.9699 | 75.4662 | 66.9793 | 63.9738 | 4411 | 1434 | 4785 | 2359 | 1346 | 57.0581 | |
| mlin-fermikit | SNP | * | map_l250_m1_e0 | homalt | 51.7475 | 41.7783 | 67.9657 | 72.7453 | 1029 | 1434 | 1029 | 485 | 445 | 91.7526 | |
| mlin-fermikit | SNP | tv | map_l250_m2_e1 | het | 42.3276 | 27.0229 | 97.6103 | 84.4394 | 531 | 1434 | 531 | 13 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 91.7011 | 87.0959 | 96.8206 | 45.2421 | 9672 | 1433 | 2223 | 73 | 72 | 98.6301 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 4.0857 | 0.0000 | 0.0000 | 61 | 1432 | 0 | 0 | 0 | ||
| jmaeng-gatk | SNP | * | map_l250_m2_e0 | homalt | 63.6387 | 46.6865 | 99.9203 | 93.0743 | 1254 | 1432 | 1254 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 93.3161 | 87.6212 | 99.8027 | 73.3610 | 10122 | 1430 | 10118 | 20 | 17 | 85.0000 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 93.3161 | 87.6212 | 99.8027 | 73.3610 | 10122 | 1430 | 10118 | 20 | 17 | 85.0000 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 75.3753 | 83.0063 | 69.0293 | 65.5447 | 6980 | 1429 | 5639 | 2530 | 425 | 16.7984 | |
| ckim-vqsr | INDEL | I1_5 | * | * | 99.3579 | 99.0515 | 99.6662 | 59.3791 | 149235 | 1429 | 149282 | 500 | 397 | 79.4000 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 36.8196 | 27.4987 | 55.6992 | 44.8224 | 542 | 1429 | 1852 | 1473 | 1170 | 79.4297 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 36.8196 | 27.4987 | 55.6992 | 44.8224 | 542 | 1429 | 1852 | 1473 | 1170 | 79.4297 | |
| ckim-gatk | SNP | * | map_l250_m2_e0 | homalt | 63.7586 | 46.7982 | 100.0000 | 93.4789 | 1257 | 1429 | 1257 | 0 | 0 | ||
| jmaeng-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.8577 | 98.4881 | 99.2301 | 73.8561 | 93021 | 1428 | 92930 | 721 | 622 | 86.2691 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 37.9771 | 33.2554 | 44.2615 | 81.8105 | 711 | 1427 | 860 | 1083 | 11 | 1.0157 | |
| ltrigg-rtg1 | INDEL | * | HG002complexvar | * | 98.8636 | 98.1465 | 99.5912 | 55.0476 | 75511 | 1426 | 75278 | 309 | 190 | 61.4887 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 35.8287 | 33.0357 | 39.1376 | 73.2950 | 703 | 1425 | 708 | 1101 | 1085 | 98.5468 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 78.4414 | 76.5741 | 80.4020 | 77.5023 | 4658 | 1425 | 4800 | 1170 | 1056 | 90.2564 | |
| anovak-vg | SNP | tv | map_l100_m2_e1 | homalt | 91.3691 | 84.6807 | 99.2047 | 63.3275 | 7877 | 1425 | 7859 | 63 | 46 | 73.0159 | |
| gduggal-snapplat | SNP | ti | HG002compoundhet | * | 85.7906 | 91.8526 | 80.4793 | 50.9850 | 16054 | 1424 | 16120 | 3910 | 442 | 11.3043 | |
| gduggal-snapplat | SNP | ti | map_l100_m1_e0 | het | 95.4495 | 95.2475 | 95.6523 | 78.8806 | 28519 | 1423 | 28557 | 1298 | 664 | 51.1556 | |
| gduggal-bwaplat | SNP | ti | HG002compoundhet | * | 89.0817 | 91.8641 | 86.4629 | 42.2720 | 16056 | 1422 | 16121 | 2524 | 263 | 10.4200 | |
| gduggal-bwafb | SNP | tv | * | * | 99.7254 | 99.8534 | 99.5978 | 25.3671 | 968276 | 1422 | 968379 | 3911 | 282 | 7.2104 | |
| mlin-fermikit | SNP | tv | map_l250_m2_e0 | het | 41.9263 | 26.7010 | 97.5518 | 84.3317 | 518 | 1422 | 518 | 13 | 0 | 0.0000 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 72.8692 | 95.0543 | 59.0803 | 78.2168 | 27292 | 1420 | 27789 | 19247 | 483 | 2.5095 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 72.8692 | 95.0543 | 59.0803 | 78.2168 | 27292 | 1420 | 27789 | 19247 | 483 | 2.5095 | |
| egarrison-hhga | INDEL | D16_PLUS | * | * | 85.6324 | 79.0831 | 93.3644 | 63.5644 | 5365 | 1419 | 5417 | 385 | 330 | 85.7143 | |
| ciseli-custom | SNP | ti | map_l125_m2_e1 | homalt | 88.7321 | 87.6244 | 89.8682 | 67.8893 | 10040 | 1418 | 10023 | 1130 | 915 | 80.9735 | |
| anovak-vg | SNP | tv | map_l100_m2_e0 | homalt | 91.3367 | 84.6212 | 99.2099 | 63.3369 | 7797 | 1417 | 7785 | 62 | 46 | 74.1935 | |
| gduggal-snapfb | INDEL | I1_5 | * | homalt | 97.0924 | 97.6551 | 96.5362 | 55.2565 | 59011 | 1417 | 59057 | 2119 | 998 | 47.0977 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 93.5778 | 91.1697 | 96.1165 | 54.9134 | 14630 | 1417 | 15642 | 632 | 605 | 95.7278 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 72.0146 | 63.6573 | 82.8979 | 66.4923 | 2482 | 1417 | 2443 | 504 | 406 | 80.5556 | |
| mlin-fermikit | INDEL | I16_PLUS | * | * | 82.9403 | 77.8109 | 88.7937 | 66.6528 | 4962 | 1415 | 4976 | 628 | 607 | 96.6561 | |
| ckim-isaac | INDEL | I6_15 | * | het | 88.7567 | 85.9065 | 91.8024 | 48.2080 | 8619 | 1414 | 8623 | 770 | 554 | 71.9481 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 62.8647 | 0.0000 | 0.0000 | 2392 | 1413 | 0 | 0 | 0 | ||
| gduggal-snapfb | SNP | * | map_l125_m2_e0 | * | 96.9292 | 96.9758 | 96.8828 | 74.5886 | 45310 | 1413 | 45314 | 1458 | 623 | 42.7298 | |
| gduggal-snapfb | SNP | * | map_l125_m2_e1 | * | 96.9532 | 97.0065 | 96.9000 | 74.6410 | 45789 | 1413 | 45793 | 1465 | 623 | 42.5256 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 79.8732 | 68.2411 | 96.2857 | 80.2619 | 3034 | 1412 | 3033 | 117 | 59 | 50.4274 | |
| ciseli-custom | SNP | ti | map_l125_m2_e0 | homalt | 88.6940 | 87.5770 | 89.8399 | 67.8832 | 9947 | 1411 | 9930 | 1123 | 909 | 80.9439 | |
| anovak-vg | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 20.3275 | 0.0000 | 0.0000 | 360 | 1411 | 0 | 0 | 0 | ||
| anovak-vg | SNP | tv | map_l100_m1_e0 | homalt | 91.2106 | 84.4078 | 99.2060 | 60.5879 | 7633 | 1410 | 7622 | 61 | 45 | 73.7705 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 57.4807 | 40.4480 | 99.2929 | 38.4711 | 957 | 1409 | 983 | 7 | 6 | 85.7143 | |
| gduggal-snapfb | SNP | * | map_l125_m1_e0 | * | 96.8640 | 96.8959 | 96.8321 | 72.7854 | 43920 | 1407 | 43924 | 1437 | 620 | 43.1454 | |
| ckim-gatk | SNP | ti | map_l150_m0_e0 | homalt | 65.8246 | 49.0764 | 99.9263 | 84.8914 | 1355 | 1406 | 1355 | 1 | 1 | 100.0000 | |
| ckim-isaac | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.8280 | 94.9712 | 98.7588 | 48.1636 | 26553 | 1406 | 26734 | 336 | 168 | 50.0000 | |
| ckim-isaac | SNP | ti | map_l250_m1_e0 | het | 68.7954 | 52.6280 | 99.3007 | 91.8721 | 1562 | 1406 | 1562 | 11 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 80.2083 | 71.8944 | 90.6965 | 69.6512 | 3594 | 1405 | 3646 | 374 | 325 | 86.8984 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 80.2083 | 71.8944 | 90.6965 | 69.6512 | 3594 | 1405 | 3646 | 374 | 325 | 86.8984 | |
| ckim-vqsr | SNP | ti | map_l250_m1_e0 | het | 68.5076 | 52.6617 | 97.9937 | 97.0232 | 1563 | 1405 | 1563 | 32 | 0 | 0.0000 | |
| eyeh-varpipe | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 73.9522 | 65.2228 | 85.3794 | 65.4520 | 2635 | 1405 | 2914 | 499 | 370 | 74.1483 | |