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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
8401-8450 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.8082 | 93.8528 | 99.9557 | 28.4115 | 6733 | 441 | 6775 | 3 | 2 | 66.6667 | |
| anovak-vg | SNP | ti | map_l250_m2_e1 | het | 72.2384 | 86.6323 | 61.9461 | 92.2704 | 2858 | 441 | 2852 | 1752 | 393 | 22.4315 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.8256 | 97.5251 | 96.1361 | 70.1065 | 17378 | 441 | 18561 | 746 | 415 | 55.6300 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9093 | 97.5848 | 98.2359 | 39.6520 | 17818 | 441 | 17820 | 320 | 305 | 95.3125 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 78.3824 | 64.7764 | 99.2239 | 34.3044 | 811 | 441 | 895 | 7 | 4 | 57.1429 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1729 | 98.6761 | 99.6748 | 69.3950 | 32796 | 440 | 42603 | 139 | 118 | 84.8921 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 84.3637 | 87.9716 | 81.0401 | 48.2088 | 3218 | 440 | 3257 | 762 | 318 | 41.7323 | |
| ciseli-custom | INDEL | D1_5 | map_l100_m1_e0 | * | 79.6470 | 76.1905 | 83.4320 | 87.8636 | 1408 | 440 | 1410 | 280 | 137 | 48.9286 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 19.0690 | 11.4688 | 56.5315 | 43.2950 | 57 | 440 | 251 | 193 | 191 | 98.9637 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 66.0791 | 54.5455 | 83.7981 | 68.9868 | 528 | 440 | 631 | 122 | 64 | 52.4590 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 97.0455 | 94.6164 | 99.6025 | 28.0867 | 7733 | 440 | 7768 | 31 | 29 | 93.5484 | |
| jlack-gatk | SNP | ti | map_l100_m2_e1 | * | 97.5095 | 99.1108 | 95.9591 | 74.4631 | 49045 | 440 | 49038 | 2065 | 195 | 9.4431 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.6406 | 96.4859 | 98.8233 | 61.6023 | 12081 | 440 | 11926 | 142 | 130 | 91.5493 | |
| anovak-vg | INDEL | I1_5 | segdup | * | 58.1085 | 58.4514 | 57.7697 | 94.2442 | 619 | 440 | 632 | 462 | 397 | 85.9307 | |
| anovak-vg | INDEL | * | map_l125_m2_e1 | het | 70.9268 | 68.8210 | 73.1655 | 89.5197 | 969 | 439 | 1017 | 373 | 101 | 27.0777 | |
| astatham-gatk | SNP | tv | map_l150_m0_e0 | het | 91.2506 | 84.5586 | 99.0928 | 85.6322 | 2404 | 439 | 2403 | 22 | 3 | 13.6364 | |
| asubramanian-gatk | INDEL | * | map_l100_m1_e0 | * | 92.0378 | 87.7579 | 96.7564 | 95.8853 | 3147 | 439 | 3162 | 106 | 17 | 16.0377 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 79.0557 | 93.1620 | 68.6595 | 75.7645 | 5981 | 439 | 5926 | 2705 | 2382 | 88.0591 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 79.0557 | 93.1620 | 68.6595 | 75.7645 | 5981 | 439 | 5926 | 2705 | 2382 | 88.0591 | |
| gduggal-bwavard | SNP | * | segdup | het | 98.1974 | 97.4649 | 98.9410 | 94.6418 | 16878 | 439 | 16724 | 179 | 23 | 12.8492 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 439 | 0 | 0 | 0 | |||
| ckim-isaac | INDEL | * | map_l125_m2_e0 | het | 80.7469 | 68.4400 | 98.4504 | 89.8946 | 952 | 439 | 953 | 15 | 5 | 33.3333 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 42.4936 | 32.3575 | 61.8768 | 70.3993 | 210 | 439 | 211 | 130 | 89 | 68.4615 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 85.2537 | 79.1052 | 92.4385 | 53.9790 | 1662 | 439 | 1577 | 129 | 123 | 95.3488 | |
| gduggal-snapfb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 439 | 0 | 0 | 0 | |||
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 71.4799 | 62.8596 | 82.8402 | 34.4961 | 743 | 439 | 140 | 29 | 29 | 100.0000 | |
| gduggal-snapplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 439 | 0 | 0 | 0 | |||
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 49.4454 | 86.5913 | 34.6019 | 50.3848 | 2835 | 439 | 2855 | 5396 | 5373 | 99.5738 | |
| ltrigg-rtg1 | SNP | ti | HG002compoundhet | * | 98.6394 | 97.4883 | 99.8180 | 33.8383 | 17039 | 439 | 17003 | 31 | 12 | 38.7097 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 0.0000 | 0.2278 | 0.0000 | 0.0000 | 1 | 438 | 0 | 0 | 0 | ||
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 13.8244 | 10.6122 | 19.8251 | 85.5882 | 52 | 438 | 68 | 275 | 74 | 26.9091 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 66.3215 | 73.5347 | 60.3969 | 44.0745 | 1217 | 438 | 1978 | 1297 | 975 | 75.1735 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 0.0000 | 0.2278 | 0.0000 | 0.0000 | 1 | 438 | 0 | 0 | 0 | ||
| gduggal-bwavard | INDEL | * | HG002compoundhet | het | 23.2106 | 89.3014 | 13.3387 | 58.9532 | 3656 | 438 | 3793 | 24643 | 23937 | 97.1351 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 0.0000 | 5.1948 | 0.0000 | 0.0000 | 24 | 438 | 0 | 0 | 0 | ||
| cchapple-custom | SNP | ti | map_l100_m0_e0 | het | 96.2084 | 96.8676 | 95.5581 | 74.9532 | 13545 | 438 | 13553 | 630 | 172 | 27.3016 | |
| jlack-gatk | SNP | * | map_l100_m0_e0 | * | 95.5864 | 98.6663 | 92.6930 | 78.0628 | 32403 | 438 | 32399 | 2554 | 207 | 8.1049 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.5494 | 92.7996 | 96.3665 | 60.4456 | 5645 | 438 | 5543 | 209 | 197 | 94.2584 | |
| jlack-gatk | SNP | ti | map_l100_m2_e0 | * | 97.4962 | 99.1075 | 95.9365 | 74.4561 | 48524 | 437 | 48517 | 2055 | 194 | 9.4404 | |
| gduggal-bwaplat | INDEL | * | map_l125_m0_e0 | * | 66.9676 | 50.4535 | 99.5526 | 96.3322 | 445 | 437 | 445 | 2 | 0 | 0.0000 | |
| anovak-vg | SNP | ti | map_l250_m2_e0 | het | 72.1503 | 86.5704 | 61.8482 | 92.2282 | 2817 | 437 | 2811 | 1734 | 389 | 22.4337 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6849 | 97.2767 | 98.0965 | 60.4473 | 15610 | 437 | 15615 | 303 | 282 | 93.0693 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 86.3348 | 92.1922 | 81.1772 | 59.7644 | 5160 | 437 | 5158 | 1196 | 1175 | 98.2441 | |
| qzeng-custom | INDEL | I6_15 | * | het | 91.4351 | 95.6444 | 87.5806 | 52.1449 | 9596 | 437 | 11812 | 1675 | 583 | 34.8060 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 33.4604 | 24.1319 | 54.5455 | 71.7587 | 139 | 437 | 120 | 100 | 1 | 1.0000 | |
| gduggal-snapfb | SNP | * | map_l125_m0_e0 | homalt | 96.2940 | 93.4893 | 99.2723 | 82.1168 | 6275 | 437 | 6275 | 46 | 16 | 34.7826 | |
| gduggal-snapfb | SNP | * | map_l250_m2_e1 | * | 94.6649 | 94.5286 | 94.8016 | 89.9551 | 7550 | 437 | 7550 | 414 | 185 | 44.6860 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 0.0000 | 0.6834 | 0.0000 | 0.0000 | 3 | 436 | 0 | 0 | 0 | ||
| gduggal-snapplat | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 0.0000 | 0.0000 | 0.0000 | 0 | 436 | 0 | 0 | 0 | |||
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 82.2614 | 82.5180 | 82.0064 | 76.8116 | 2058 | 436 | 2060 | 452 | 11 | 2.4336 | |