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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
69151-69200 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | * | map_l100_m1_e0 | het | 83.9386 | 73.4228 | 97.9701 | 85.4069 | 1641 | 594 | 1641 | 34 | 14 | 41.1765 | |
| anovak-vg | SNP | * | map_l250_m0_e0 | * | 72.9992 | 77.5176 | 68.9786 | 95.8110 | 1655 | 480 | 1641 | 738 | 163 | 22.0867 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 94.8534 | 92.9705 | 96.8142 | 85.5904 | 1640 | 124 | 1641 | 54 | 22 | 40.7407 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.4854 | 99.3353 | 99.6359 | 61.3327 | 1644 | 11 | 1642 | 6 | 3 | 50.0000 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.4553 | 99.3353 | 99.5755 | 60.7194 | 1644 | 11 | 1642 | 7 | 4 | 57.1429 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 83.2354 | 82.2465 | 84.2483 | 57.4547 | 1728 | 373 | 1642 | 307 | 301 | 98.0456 | |
| rpoplin-dv42 | INDEL | I1_5 | HG002complexvar | hetalt | 96.6129 | 94.0904 | 99.2745 | 71.2548 | 1624 | 102 | 1642 | 12 | 11 | 91.6667 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.4556 | 99.3958 | 99.5154 | 60.4361 | 1645 | 10 | 1643 | 8 | 5 | 62.5000 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.4857 | 99.3958 | 99.5758 | 60.5358 | 1645 | 10 | 1643 | 7 | 4 | 57.1429 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.5462 | 99.4562 | 99.6364 | 61.3039 | 1646 | 9 | 1644 | 6 | 3 | 50.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 90.1124 | 96.0968 | 84.8297 | 79.1299 | 1748 | 71 | 1644 | 294 | 276 | 93.8776 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 90.1124 | 96.0968 | 84.8297 | 79.1299 | 1748 | 71 | 1644 | 294 | 276 | 93.8776 | |
| gduggal-snapfb | INDEL | I1_5 | map_siren | het | 94.9188 | 96.2522 | 93.6219 | 81.5720 | 1618 | 63 | 1644 | 112 | 17 | 15.1786 | |
| gduggal-bwafb | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.0894 | 97.2749 | 98.9176 | 66.3428 | 1642 | 46 | 1645 | 18 | 16 | 88.8889 | |
| ckim-isaac | INDEL | D16_PLUS | HG002compoundhet | hetalt | 86.1574 | 76.3485 | 98.8582 | 24.5694 | 1472 | 456 | 1645 | 19 | 17 | 89.4737 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 94.5501 | 90.3525 | 99.1566 | 32.4379 | 1461 | 156 | 1646 | 14 | 14 | 100.0000 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 84.2444 | 82.4369 | 86.1329 | 57.6838 | 1732 | 369 | 1646 | 265 | 260 | 98.1132 | |
| gduggal-bwafb | INDEL | I1_5 | map_siren | het | 97.2030 | 95.6573 | 98.7995 | 79.6283 | 1608 | 73 | 1646 | 20 | 10 | 50.0000 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.1748 | 98.8355 | 99.5163 | 68.9098 | 1358 | 16 | 1646 | 8 | 6 | 75.0000 | |
| cchapple-custom | INDEL | C1_5 | HG002complexvar | het | 90.6065 | 85.7143 | 96.0910 | 77.9776 | 6 | 1 | 1647 | 67 | 24 | 35.8209 | |
| gduggal-snapvard | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.7991 | 95.5378 | 98.0941 | 72.6859 | 1670 | 78 | 1647 | 32 | 12 | 37.5000 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.6020 | 89.7937 | 95.5916 | 62.8768 | 1654 | 188 | 1648 | 76 | 46 | 60.5263 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 85.1654 | 74.5662 | 99.2771 | 27.6058 | 1633 | 557 | 1648 | 12 | 9 | 75.0000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.8248 | 88.7486 | 99.5169 | 32.2699 | 1617 | 205 | 1648 | 8 | 8 | 100.0000 | |
| asubramanian-gatk | SNP | ti | map_l150_m2_e1 | homalt | 35.3029 | 21.4351 | 100.0000 | 91.9163 | 1649 | 6044 | 1649 | 0 | 0 | ||
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 79.6057 | 84.7414 | 75.0569 | 26.8642 | 1655 | 298 | 1649 | 548 | 546 | 99.6350 | |
| ciseli-custom | INDEL | * | map_l100_m2_e0 | het | 73.2740 | 70.9580 | 75.7464 | 88.9861 | 1637 | 670 | 1649 | 528 | 311 | 58.9015 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 92.8267 | 87.4867 | 98.8609 | 64.0750 | 1650 | 236 | 1649 | 19 | 5 | 26.3158 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 93.4043 | 94.3966 | 92.4327 | 50.2787 | 438 | 26 | 1649 | 135 | 36 | 26.6667 | |
| cchapple-custom | INDEL | C1_5 | * | het | 91.7367 | 88.8889 | 94.7731 | 92.2595 | 8 | 1 | 1650 | 91 | 24 | 26.3736 | |
| anovak-vg | INDEL | D1_5 | map_l100_m2_e0 | * | 84.6007 | 85.6397 | 83.5866 | 84.4811 | 1640 | 275 | 1650 | 324 | 122 | 37.6543 | |
| gduggal-snapvard | SNP | ti | map_l250_m2_e1 | homalt | 96.5718 | 93.8488 | 99.4575 | 88.0802 | 1663 | 109 | 1650 | 9 | 7 | 77.7778 | |
| ndellapenna-hhga | INDEL | I1_5 | map_siren | het | 98.8036 | 98.2748 | 99.3381 | 80.3824 | 1652 | 29 | 1651 | 11 | 1 | 9.0909 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.7305 | 89.6851 | 98.1581 | 66.4808 | 1652 | 190 | 1652 | 31 | 17 | 54.8387 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.9517 | 89.0231 | 99.4582 | 32.2317 | 1622 | 200 | 1652 | 9 | 8 | 88.8889 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.8671 | 89.7394 | 98.3929 | 66.3731 | 1653 | 189 | 1653 | 27 | 15 | 55.5556 | |
| anovak-vg | INDEL | * | map_l100_m2_e1 | het | 70.6838 | 66.8374 | 75.0000 | 86.9385 | 1566 | 777 | 1653 | 551 | 156 | 28.3122 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 73.4894 | 61.2085 | 91.9355 | 34.5468 | 1013 | 642 | 1653 | 145 | 143 | 98.6207 | |
| ghariani-varprowl | INDEL | I1_5 | map_siren | het | 93.1801 | 98.4533 | 88.4430 | 87.0613 | 1655 | 26 | 1653 | 216 | 106 | 49.0741 | |
| hfeng-pmm1 | INDEL | I1_5 | map_siren | het | 98.8017 | 98.0369 | 99.5786 | 80.1885 | 1648 | 33 | 1654 | 7 | 0 | 0.0000 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 84.8488 | 74.6492 | 98.2769 | 53.8272 | 1649 | 560 | 1654 | 29 | 24 | 82.7586 | |
| raldana-dualsentieon | INDEL | I1_5 | map_siren | het | 98.5075 | 98.0369 | 98.9826 | 78.7269 | 1648 | 33 | 1654 | 17 | 1 | 5.8824 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 87.1624 | 85.4630 | 88.9307 | 63.9481 | 1652 | 281 | 1655 | 206 | 205 | 99.5146 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 96.7286 | 97.2989 | 96.1650 | 69.1079 | 1657 | 46 | 1655 | 66 | 14 | 21.2121 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 61.4567 | 89.8526 | 46.6986 | 86.2385 | 1585 | 179 | 1655 | 1889 | 13 | 0.6882 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 95.9181 | 92.2078 | 99.9396 | 36.0371 | 1633 | 138 | 1655 | 1 | 1 | 100.0000 | |
| eyeh-varpipe | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.4962 | 98.9130 | 94.1946 | 61.4016 | 1729 | 19 | 1655 | 102 | 27 | 26.4706 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.8776 | 89.9023 | 98.2206 | 65.9944 | 1656 | 186 | 1656 | 30 | 21 | 70.0000 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 74.9362 | 87.5375 | 65.5063 | 57.1453 | 1166 | 166 | 1656 | 872 | 119 | 13.6468 | |
| eyeh-varpipe | INDEL | * | map_l125_m1_e0 | het | 96.7178 | 96.4794 | 96.9573 | 84.9956 | 1288 | 47 | 1657 | 52 | 30 | 57.6923 | |