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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
80851-80900 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | * | HG002complexvar | homalt | 93.1685 | 88.5818 | 98.2561 | 47.1228 | 23941 | 3086 | 23890 | 424 | 132 | 31.1321 | |
| bgallagher-sentieon | INDEL | I6_15 | HG002compoundhet | * | 93.1478 | 91.3856 | 94.9793 | 37.0668 | 8020 | 756 | 8021 | 424 | 422 | 99.5283 | |
| bgallagher-sentieon | SNP | * | map_l125_m2_e1 | * | 99.2798 | 99.4555 | 99.1048 | 72.9953 | 46945 | 257 | 46939 | 424 | 70 | 16.5094 | |
| anovak-vg | INDEL | * | map_l150_m1_e0 | * | 72.5622 | 74.5142 | 70.7099 | 89.9578 | 997 | 341 | 1026 | 425 | 224 | 52.7059 | |
| gduggal-snapfb | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 88.4727 | 98.6270 | 80.2142 | 81.5986 | 1724 | 24 | 1723 | 425 | 22 | 5.1765 | |
| gduggal-snapfb | SNP | tv | map_l100_m0_e0 | het | 95.8604 | 97.4661 | 94.3068 | 70.6611 | 7039 | 183 | 7040 | 425 | 163 | 38.3529 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 91.7774 | 93.1267 | 90.4666 | 45.7994 | 691 | 51 | 4033 | 425 | 374 | 88.0000 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 79.2418 | 93.0939 | 68.9781 | 57.8721 | 337 | 25 | 945 | 425 | 175 | 41.1765 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.7235 | 93.8350 | 95.6289 | 69.0222 | 9452 | 621 | 9298 | 425 | 390 | 91.7647 | |
| jpowers-varprowl | SNP | tv | map_l125_m1_e0 | * | 97.1666 | 96.9968 | 97.3371 | 76.5818 | 15535 | 481 | 15535 | 425 | 117 | 27.5294 | |
| ciseli-custom | SNP | * | map_l250_m2_e1 | homalt | 81.0638 | 78.8447 | 83.4114 | 87.8871 | 2143 | 575 | 2137 | 425 | 307 | 72.2353 | |
| gduggal-bwafb | SNP | ti | map_l100_m2_e1 | het | 98.8201 | 99.0084 | 98.6326 | 70.6269 | 30653 | 307 | 30655 | 425 | 95 | 22.3529 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 74.6828 | 72.3465 | 77.1751 | 57.2642 | 1520 | 581 | 1437 | 425 | 403 | 94.8235 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 88.0210 | 92.7552 | 83.7467 | 49.6639 | 2535 | 198 | 2195 | 426 | 362 | 84.9765 | |
| gduggal-snapfb | SNP | tv | map_l150_m1_e0 | het | 95.6989 | 97.3798 | 94.0751 | 75.4297 | 6764 | 182 | 6764 | 426 | 173 | 40.6103 | |
| ghariani-varprowl | INDEL | * | map_l100_m2_e0 | het | 90.5891 | 98.0928 | 84.1518 | 89.9495 | 2263 | 44 | 2262 | 426 | 198 | 46.4789 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 38.2525 | 82.8402 | 24.8677 | 55.3895 | 140 | 29 | 141 | 426 | 425 | 99.7653 | |
| gduggal-snapplat | SNP | * | map_l250_m2_e0 | * | 87.8865 | 82.6252 | 93.8634 | 93.9104 | 6515 | 1370 | 6516 | 426 | 206 | 48.3568 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 78.1683 | 81.1429 | 75.4042 | 51.8889 | 852 | 198 | 1306 | 426 | 326 | 76.5258 | |
| qzeng-custom | INDEL | * | map_l100_m1_e0 | * | 83.9800 | 79.0296 | 89.5920 | 87.4621 | 2834 | 752 | 3667 | 426 | 66 | 15.4930 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 86.6995 | 85.5368 | 87.8943 | 72.5250 | 3099 | 524 | 3093 | 426 | 415 | 97.4178 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.0265 | 98.4792 | 97.5780 | 71.1859 | 17548 | 271 | 17163 | 426 | 391 | 91.7840 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 76.6125 | 83.7838 | 70.5720 | 29.6655 | 589 | 114 | 1024 | 427 | 379 | 88.7588 | |
| gduggal-snapplat | SNP | * | map_l250_m2_e1 | het | 87.7421 | 84.4985 | 91.2446 | 94.9087 | 4448 | 816 | 4450 | 427 | 204 | 47.7752 | |
| anovak-vg | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 93.6443 | 95.4077 | 91.9449 | 64.3247 | 4633 | 223 | 4874 | 427 | 230 | 53.8642 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 92.4707 | 95.9016 | 89.2767 | 52.5444 | 468 | 20 | 3555 | 427 | 343 | 80.3279 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 60.0572 | 82.6840 | 47.1535 | 44.1989 | 382 | 80 | 381 | 427 | 422 | 98.8290 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.5538 | 96.1694 | 98.9788 | 57.8031 | 41675 | 1660 | 41482 | 428 | 360 | 84.1121 | |
| raldana-dualsentieon | SNP | ti | map_siren | * | 99.5625 | 99.5516 | 99.5734 | 52.8084 | 99905 | 450 | 99890 | 428 | 23 | 5.3738 | |
| egarrison-hhga | SNP | tv | * | * | 99.8815 | 99.8074 | 99.9558 | 20.9138 | 967822 | 1868 | 967852 | 428 | 112 | 26.1682 | |
| bgallagher-sentieon | SNP | ti | map_siren | het | 99.4766 | 99.6377 | 99.3160 | 56.6817 | 62156 | 226 | 62147 | 428 | 50 | 11.6822 | |
| ckim-dragen | SNP | * | HG002complexvar | het | 99.9146 | 99.9212 | 99.9081 | 19.1598 | 465130 | 367 | 465401 | 428 | 195 | 45.5607 | |
| ckim-dragen | INDEL | I1_5 | HG002compoundhet | * | 94.8982 | 93.4283 | 96.4151 | 65.5477 | 11544 | 812 | 11538 | 429 | 425 | 99.0676 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 20.1055 | 12.5225 | 50.9714 | 65.7132 | 488 | 3409 | 446 | 429 | 399 | 93.0070 | |
| raldana-dualsentieon | SNP | * | map_l125_m2_e1 | * | 99.1573 | 99.2225 | 99.0922 | 71.3931 | 46835 | 367 | 46829 | 429 | 15 | 3.4965 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 87.9792 | 79.5523 | 98.4030 | 81.3702 | 26440 | 6796 | 26434 | 429 | 144 | 33.5664 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 95.5224 | 99.6844 | 91.6941 | 50.1544 | 4738 | 15 | 4736 | 429 | 428 | 99.7669 | |
| jpowers-varprowl | SNP | * | map_l150_m0_e0 | het | 94.6235 | 94.6474 | 94.5997 | 86.3683 | 7515 | 425 | 7515 | 429 | 135 | 31.4685 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.1076 | 98.6776 | 99.5414 | 71.9967 | 93200 | 1249 | 93118 | 429 | 358 | 83.4499 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 52.4550 | 86.9565 | 37.5546 | 88.1756 | 240 | 36 | 258 | 429 | 7 | 1.6317 | |
| gduggal-snapvard | INDEL | D1_5 | map_l100_m2_e1 | * | 88.9679 | 94.1723 | 84.3087 | 85.8664 | 1826 | 113 | 2305 | 429 | 173 | 40.3263 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.2960 | 99.5274 | 99.0657 | 69.8134 | 45486 | 216 | 45486 | 429 | 30 | 6.9930 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.2960 | 99.5274 | 99.0657 | 69.8134 | 45486 | 216 | 45486 | 429 | 30 | 6.9930 | |
| mlin-fermikit | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.0726 | 96.5229 | 95.6265 | 68.5165 | 9355 | 337 | 9380 | 429 | 282 | 65.7343 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 81.7362 | 74.1234 | 91.0918 | 40.7803 | 4397 | 1535 | 4397 | 430 | 427 | 99.3023 | |
| ndellapenna-hhga | INDEL | D1_5 | HG002complexvar | het | 97.7232 | 97.5199 | 97.9274 | 51.5698 | 20250 | 515 | 20317 | 430 | 365 | 84.8837 | |
| hfeng-pmm3 | SNP | ti | * | het | 99.9388 | 99.9112 | 99.9664 | 17.2454 | 1280753 | 1138 | 1280703 | 430 | 18 | 4.1861 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 77.2684 | 79.2312 | 75.4005 | 60.0913 | 1278 | 335 | 1318 | 430 | 259 | 60.2326 | |
| anovak-vg | INDEL | D1_5 | map_siren | het | 86.2774 | 89.9868 | 82.8617 | 80.2332 | 2049 | 228 | 2079 | 430 | 142 | 33.0233 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.7920 | 99.4303 | 96.2068 | 45.3054 | 10298 | 59 | 10906 | 430 | 320 | 74.4186 | |