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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
57451-57500 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.8475 | 99.4543 | 98.2480 | 73.3285 | 729 | 4 | 729 | 13 | 13 | 100.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.0710 | 97.8937 | 98.2489 | 60.0570 | 15709 | 338 | 15710 | 280 | 267 | 95.3571 | |
| astatham-gatk | INDEL | * | map_l100_m0_e0 | homalt | 98.7292 | 99.2141 | 98.2490 | 85.0971 | 505 | 4 | 505 | 9 | 5 | 55.5556 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l150_m2_e0 | het | 98.0541 | 97.8599 | 98.2490 | 88.2809 | 503 | 11 | 505 | 9 | 2 | 22.2222 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 68.4973 | 52.5761 | 98.2495 | 47.4411 | 898 | 810 | 898 | 16 | 15 | 93.7500 | |
| raldana-dualsentieon | SNP | * | map_l125_m0_e0 | het | 98.3431 | 98.4365 | 98.2499 | 76.1833 | 12466 | 198 | 12463 | 222 | 2 | 0.9009 | |
| ckim-gatk | SNP | * | map_l100_m2_e1 | * | 89.5170 | 82.2096 | 98.2503 | 79.5686 | 61441 | 13296 | 61430 | 1094 | 86 | 7.8611 | |
| gduggal-snapfb | INDEL | I1_5 | map_l125_m2_e0 | homalt | 98.6836 | 99.1202 | 98.2507 | 89.4526 | 338 | 3 | 337 | 6 | 3 | 50.0000 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.0537 | 93.9527 | 98.2507 | 73.2824 | 1709 | 110 | 1685 | 30 | 15 | 50.0000 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.0537 | 93.9527 | 98.2507 | 73.2824 | 1709 | 110 | 1685 | 30 | 15 | 50.0000 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.0298 | 97.8096 | 98.2511 | 71.9586 | 3483 | 78 | 3483 | 62 | 54 | 87.0968 | |
| jli-custom | INDEL | * | map_l125_m0_e0 | homalt | 98.5965 | 98.9437 | 98.2517 | 86.9644 | 281 | 3 | 281 | 5 | 4 | 80.0000 | |
| hfeng-pmm1 | INDEL | * | map_l125_m0_e0 | homalt | 98.5965 | 98.9437 | 98.2517 | 86.4967 | 281 | 3 | 281 | 5 | 3 | 60.0000 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 75.9688 | 61.9247 | 98.2517 | 67.2018 | 296 | 182 | 281 | 5 | 5 | 100.0000 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.4267 | 96.6141 | 98.2531 | 76.5682 | 2083 | 73 | 2081 | 37 | 19 | 51.3514 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.8396 | 93.5417 | 98.2533 | 81.8470 | 449 | 31 | 450 | 8 | 7 | 87.5000 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.9533 | 95.6873 | 98.2533 | 72.2760 | 710 | 32 | 675 | 12 | 7 | 58.3333 | |
| egarrison-hhga | INDEL | I16_PLUS | * | hetalt | 90.0034 | 83.0315 | 98.2535 | 51.8970 | 1742 | 356 | 1744 | 31 | 26 | 83.8710 | |
| jpowers-varprowl | SNP | * | map_siren | het | 98.0429 | 97.8328 | 98.2539 | 63.2948 | 89019 | 1972 | 89021 | 1582 | 312 | 19.7219 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.6864 | 99.1226 | 98.2540 | 71.3658 | 3728 | 33 | 3714 | 66 | 64 | 96.9697 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.6864 | 99.1226 | 98.2540 | 71.3658 | 3728 | 33 | 3714 | 66 | 64 | 96.9697 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.5000 | 98.7469 | 98.2544 | 65.8723 | 394 | 5 | 394 | 7 | 5 | 71.4286 | |
| hfeng-pmm1 | INDEL | * | map_l100_m0_e0 | * | 97.6521 | 97.0569 | 98.2547 | 83.9206 | 1517 | 46 | 1520 | 27 | 6 | 22.2222 | |
| astatham-gatk | INDEL | I1_5 | map_l150_m0_e0 | * | 96.8349 | 95.4545 | 98.2558 | 92.5054 | 168 | 8 | 169 | 3 | 2 | 66.6667 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.9710 | 97.6879 | 98.2558 | 68.8688 | 338 | 8 | 338 | 6 | 0 | 0.0000 | |
| ckim-isaac | INDEL | * | HG002complexvar | homalt | 93.1685 | 88.5818 | 98.2561 | 47.1228 | 23941 | 3086 | 23890 | 424 | 132 | 31.1321 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.0769 | 99.9113 | 98.2563 | 59.2395 | 1127 | 1 | 1127 | 20 | 10 | 50.0000 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.6411 | 95.0774 | 98.2571 | 84.2376 | 1352 | 70 | 1353 | 24 | 15 | 62.5000 | |
| hfeng-pmm2 | INDEL | * | map_l125_m0_e0 | homalt | 98.7741 | 99.2958 | 98.2578 | 86.8469 | 282 | 2 | 282 | 5 | 4 | 80.0000 | |
| hfeng-pmm3 | INDEL | * | map_l125_m0_e0 | homalt | 98.7741 | 99.2958 | 98.2578 | 85.7498 | 282 | 2 | 282 | 5 | 3 | 60.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l100_m0_e0 | * | 98.0857 | 97.9143 | 98.2578 | 84.7960 | 845 | 18 | 846 | 15 | 6 | 40.0000 | |
| ckim-gatk | INDEL | * | map_l125_m0_e0 | homalt | 98.7741 | 99.2958 | 98.2578 | 88.6874 | 282 | 2 | 282 | 5 | 4 | 80.0000 | |
| ckim-vqsr | SNP | tv | map_l125_m2_e0 | het | 80.8052 | 68.6171 | 98.2581 | 89.8954 | 7165 | 3277 | 7164 | 127 | 1 | 0.7874 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.3938 | 98.5294 | 98.2585 | 65.1438 | 1072 | 16 | 1072 | 19 | 14 | 73.6842 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l125_m1_e0 | * | 98.3020 | 98.3456 | 98.2585 | 85.8752 | 1070 | 18 | 1072 | 19 | 8 | 42.1053 | |
| ghariani-varprowl | SNP | tv | func_cds | het | 99.0291 | 99.8118 | 98.2586 | 43.0471 | 2652 | 5 | 2652 | 47 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | D1_5 | map_siren | het | 98.2729 | 98.2872 | 98.2586 | 80.4710 | 2238 | 39 | 2257 | 40 | 2 | 5.0000 | |
| ltrigg-rtg1 | SNP | tv | func_cds | het | 99.0291 | 99.8118 | 98.2586 | 27.7763 | 2652 | 5 | 2652 | 47 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | * | map_l100_m2_e1 | * | 96.0874 | 94.0096 | 98.2592 | 84.3618 | 3531 | 225 | 3556 | 63 | 22 | 34.9206 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.7633 | 97.2714 | 98.2602 | 58.6360 | 30551 | 857 | 30554 | 541 | 494 | 91.3124 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.7633 | 97.2714 | 98.2602 | 58.6360 | 30551 | 857 | 30554 | 541 | 494 | 91.3124 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 90.4376 | 83.7686 | 98.2603 | 35.1614 | 1636 | 317 | 1638 | 29 | 15 | 51.7241 | |
| gduggal-snapfb | SNP | tv | func_cds | het | 99.0857 | 99.9247 | 98.2605 | 37.4682 | 2655 | 2 | 2655 | 47 | 0 | 0.0000 | |
| gduggal-snapfb | INDEL | I1_5 | map_l125_m2_e1 | homalt | 98.6912 | 99.1254 | 98.2609 | 89.6084 | 340 | 3 | 339 | 6 | 3 | 50.0000 | |
| raldana-dualsentieon | INDEL | I1_5 | map_l125_m0_e0 | homalt | 98.6900 | 99.1228 | 98.2609 | 83.5479 | 113 | 1 | 113 | 2 | 1 | 50.0000 | |
| ndellapenna-hhga | INDEL | * | map_l250_m2_e1 | homalt | 97.8355 | 97.4138 | 98.2609 | 95.2243 | 113 | 3 | 113 | 2 | 1 | 50.0000 | |
| qzeng-custom | INDEL | D1_5 | map_l125_m2_e0 | homalt | 86.4651 | 77.1978 | 98.2609 | 84.8218 | 281 | 83 | 339 | 6 | 6 | 100.0000 | |
| ckim-gatk | INDEL | * | map_l250_m2_e0 | homalt | 98.2609 | 98.2609 | 98.2609 | 95.6538 | 113 | 2 | 113 | 2 | 2 | 100.0000 | |
| astatham-gatk | INDEL | D6_15 | map_l125_m1_e0 | * | 97.4138 | 96.5812 | 98.2609 | 91.2080 | 113 | 4 | 113 | 2 | 1 | 50.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | map_l125_m1_e0 | * | 97.4138 | 96.5812 | 98.2609 | 91.0991 | 113 | 4 | 113 | 2 | 1 | 50.0000 | |