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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
6901-6950 / 86044 show all | |||||||||||||||
| anovak-vg | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 90.5371 | 93.0336 | 88.1711 | 73.4829 | 1883 | 141 | 1938 | 260 | 97 | 37.3077 | |
| astatham-gatk | INDEL | I1_5 | * | homalt | 99.7125 | 99.8544 | 99.5710 | 55.1217 | 60340 | 88 | 60345 | 260 | 257 | 98.8462 | |
| dgrover-gatk | SNP | * | map_l100_m0_e0 | * | 99.2175 | 99.2266 | 99.2084 | 71.3904 | 32587 | 254 | 32583 | 260 | 57 | 21.9231 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 96.4687 | 96.5227 | 96.4148 | 36.9062 | 6995 | 252 | 6992 | 260 | 103 | 39.6154 | |
| gduggal-snapplat | INDEL | * | segdup | het | 76.3682 | 71.8281 | 81.5210 | 97.0363 | 1053 | 413 | 1147 | 260 | 13 | 5.0000 | |
| gduggal-snapvard | INDEL | D1_5 | map_l100_m0_e0 | * | 87.0777 | 95.0174 | 80.3625 | 87.2790 | 820 | 43 | 1064 | 260 | 71 | 27.3077 | |
| jpowers-varprowl | INDEL | * | map_l100_m2_e1 | * | 91.1487 | 89.5367 | 92.8197 | 85.5685 | 3363 | 393 | 3361 | 260 | 208 | 80.0000 | |
| jpowers-varprowl | INDEL | I16_PLUS | HG002complexvar | * | 64.1165 | 56.5317 | 74.0519 | 63.2294 | 740 | 569 | 742 | 260 | 258 | 99.2308 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 88.6737 | 96.3158 | 82.1551 | 76.7252 | 1281 | 49 | 1197 | 260 | 253 | 97.3077 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 72.3119 | 89.8851 | 60.4863 | 71.9881 | 391 | 44 | 398 | 260 | 35 | 13.4615 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 83.6651 | 85.4732 | 81.9319 | 70.4517 | 1165 | 198 | 1179 | 260 | 119 | 45.7692 | |
| ciseli-custom | INDEL | * | map_l100_m2_e1 | homalt | 69.4068 | 63.9344 | 75.9036 | 85.6497 | 819 | 462 | 819 | 260 | 212 | 81.5385 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 94.6758 | 93.5408 | 95.8387 | 47.4428 | 1593 | 110 | 5988 | 260 | 204 | 78.4615 | |
| gduggal-bwavard | INDEL | * | map_l100_m0_e0 | * | 89.2130 | 93.9219 | 84.9537 | 89.1607 | 1468 | 95 | 1468 | 260 | 67 | 25.7692 | |
| gduggal-bwavard | INDEL | * | map_l125_m1_e0 | het | 90.3770 | 98.4270 | 83.5443 | 91.2553 | 1314 | 21 | 1320 | 260 | 67 | 25.7692 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.1022 | 99.6257 | 98.5842 | 64.7104 | 18098 | 68 | 18104 | 260 | 243 | 93.4615 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.1022 | 99.6257 | 98.5842 | 64.7104 | 18098 | 68 | 18104 | 260 | 243 | 93.4615 | |
| hfeng-pmm2 | SNP | * | map_l150_m2_e1 | het | 98.9487 | 99.1652 | 98.7332 | 79.6403 | 20193 | 170 | 20187 | 259 | 23 | 8.8803 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 63.1909 | 86.1224 | 49.9033 | 76.4142 | 422 | 68 | 258 | 259 | 240 | 92.6641 | |
| jpowers-varprowl | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.3288 | 99.0403 | 97.6276 | 52.2232 | 10629 | 103 | 10658 | 259 | 68 | 26.2548 | |
| jpowers-varprowl | SNP | tv | map_l125_m0_e0 | het | 94.8319 | 95.4783 | 94.1941 | 83.6101 | 4202 | 199 | 4202 | 259 | 65 | 25.0965 | |
| ltrigg-rtg1 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.5600 | 99.5848 | 99.5352 | 55.2358 | 55400 | 231 | 55463 | 259 | 19 | 7.3359 | |
| egarrison-hhga | INDEL | I6_15 | * | homalt | 96.9232 | 97.9324 | 95.9347 | 48.1653 | 6110 | 129 | 6112 | 259 | 222 | 85.7143 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 86.2084 | 80.6245 | 92.6232 | 55.4837 | 3279 | 788 | 3252 | 259 | 195 | 75.2896 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1240 | 97.6833 | 98.5687 | 46.3695 | 17836 | 423 | 17837 | 259 | 256 | 98.8417 | |
| anovak-vg | INDEL | * | map_l150_m2_e0 | het | 71.4142 | 70.7506 | 72.0905 | 91.6109 | 641 | 265 | 669 | 259 | 74 | 28.5714 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.7848 | 99.4179 | 94.2876 | 66.3675 | 4270 | 25 | 4275 | 259 | 18 | 6.9498 | |
| ghariani-varprowl | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 97.9537 | 99.3610 | 96.5858 | 46.1375 | 7308 | 47 | 7327 | 259 | 42 | 16.2162 | |
| ghariani-varprowl | INDEL | D6_15 | HG002compoundhet | homalt | 13.1465 | 79.1667 | 7.1685 | 47.3585 | 19 | 5 | 20 | 259 | 232 | 89.5753 | |
| cchapple-custom | SNP | * | map_l250_m1_e0 | * | 96.0890 | 95.7906 | 96.3892 | 89.6069 | 6918 | 304 | 6914 | 259 | 62 | 23.9382 | |
| cchapple-custom | SNP | * | map_l250_m1_e0 | het | 95.0712 | 95.5205 | 94.6261 | 91.1826 | 4542 | 213 | 4543 | 258 | 61 | 23.6434 | |
| ckim-dragen | SNP | tv | map_l150_m1_e0 | het | 97.4517 | 98.5603 | 96.3677 | 80.7125 | 6846 | 100 | 6845 | 258 | 17 | 6.5892 | |
| asubramanian-gatk | INDEL | * | * | hetalt | 95.6373 | 92.5665 | 98.9188 | 59.3274 | 23361 | 1876 | 23605 | 258 | 236 | 91.4729 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.8361 | 99.3147 | 98.3621 | 62.3698 | 15652 | 108 | 15494 | 258 | 231 | 89.5349 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 85.8405 | 84.9119 | 86.7896 | 57.5804 | 1784 | 317 | 1695 | 258 | 252 | 97.6744 | |
| raldana-dualsentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 82.1683 | 78.7720 | 85.8708 | 53.3827 | 1655 | 446 | 1568 | 258 | 253 | 98.0620 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 86.4854 | 99.1784 | 76.6727 | 86.8957 | 845 | 7 | 848 | 258 | 212 | 82.1705 | |
| ndellapenna-hhga | SNP | ti | * | homalt | 99.9286 | 99.8893 | 99.9678 | 16.7330 | 802149 | 889 | 802170 | 258 | 209 | 81.0078 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.8647 | 98.5647 | 99.1665 | 69.0402 | 30696 | 447 | 30695 | 258 | 94 | 36.4341 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.8647 | 98.5647 | 99.1665 | 69.0402 | 30696 | 447 | 30695 | 258 | 94 | 36.4341 | |
| jlack-gatk | INDEL | * | map_l100_m1_e0 | het | 93.6574 | 98.2103 | 89.5079 | 89.1540 | 2195 | 40 | 2201 | 258 | 20 | 7.7519 | |
| jlack-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4351 | 99.7890 | 99.0837 | 56.5880 | 27900 | 59 | 27899 | 258 | 21 | 8.1395 | |
| ckim-vqsr | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4494 | 99.3637 | 99.5353 | 61.3550 | 55277 | 354 | 55266 | 258 | 27 | 10.4651 | |
| dgrover-gatk | SNP | * | map_l150_m1_e0 | * | 99.1521 | 99.1473 | 99.1569 | 77.1188 | 30348 | 261 | 30342 | 258 | 59 | 22.8682 | |
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 73.1437 | 60.1120 | 93.3897 | 54.7163 | 3650 | 2422 | 3645 | 258 | 193 | 74.8062 | |
| ghariani-varprowl | INDEL | I1_5 | map_siren | * | 92.4494 | 93.3444 | 91.5714 | 83.4764 | 2805 | 200 | 2803 | 258 | 121 | 46.8992 | |
| gduggal-snapfb | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 96.6308 | 99.6416 | 93.7966 | 43.2141 | 3892 | 14 | 3901 | 258 | 11 | 4.2636 | |
| gduggal-snapplat | INDEL | D1_5 | map_siren | het | 85.7607 | 82.4769 | 89.3168 | 89.6940 | 1878 | 399 | 2157 | 258 | 42 | 16.2791 | |
| gduggal-snapplat | SNP | ti | map_l250_m2_e0 | * | 88.7392 | 83.8658 | 94.2139 | 93.6830 | 4200 | 808 | 4201 | 258 | 136 | 52.7132 | |
| gduggal-bwafb | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.0382 | 97.9352 | 92.3077 | 77.3745 | 3083 | 65 | 3096 | 258 | 64 | 24.8062 | |