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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
83801-83850 / 86044 show all | |||||||||||||||
| jlack-gatk | SNP | ti | map_l100_m2_e1 | het | 96.4266 | 99.2506 | 93.7588 | 78.7315 | 30728 | 232 | 30721 | 2045 | 177 | 8.6553 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.3847 | 97.8381 | 98.9375 | 61.5106 | 30729 | 679 | 30729 | 330 | 295 | 89.3939 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.3847 | 97.8381 | 98.9375 | 61.5106 | 30729 | 679 | 30729 | 330 | 295 | 89.3939 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5126 | 99.8992 | 99.1290 | 74.4665 | 30730 | 31 | 30730 | 270 | 263 | 97.4074 | |
| ckim-dragen | SNP | ti | map_l100_m2_e1 | het | 98.1227 | 99.2603 | 97.0108 | 73.2091 | 30731 | 229 | 30734 | 947 | 88 | 9.2925 | |
| jmaeng-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4869 | 99.9155 | 99.0621 | 74.5055 | 30735 | 26 | 30735 | 291 | 281 | 96.5636 | |
| ckim-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5208 | 99.9187 | 99.1260 | 74.4622 | 30736 | 25 | 30736 | 271 | 264 | 97.4170 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6951 | 99.8992 | 99.4918 | 73.2959 | 30730 | 31 | 30737 | 157 | 151 | 96.1783 | |
| astatham-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5289 | 99.9220 | 99.1388 | 74.4236 | 30737 | 24 | 30737 | 267 | 261 | 97.7528 | |
| bgallagher-sentieon | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.3343 | 99.9317 | 98.7440 | 74.3514 | 30740 | 21 | 30740 | 391 | 384 | 98.2097 | |
| raldana-dualsentieon | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4822 | 99.9317 | 99.0367 | 73.5845 | 30740 | 21 | 30740 | 299 | 294 | 98.3278 | |
| dgrover-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5418 | 99.9350 | 99.1517 | 74.5652 | 30741 | 20 | 30741 | 263 | 257 | 97.7186 | |
| gduggal-bwavard | SNP | * | map_l150_m2_e0 | * | 94.9737 | 97.7584 | 92.3433 | 83.0785 | 31138 | 714 | 30742 | 2549 | 141 | 5.5316 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.2432 | 98.7413 | 99.7502 | 68.4984 | 30751 | 392 | 30752 | 77 | 8 | 10.3896 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.2432 | 98.7413 | 99.7502 | 68.4984 | 30751 | 392 | 30752 | 77 | 8 | 10.3896 | |
| hfeng-pmm2 | SNP | ti | map_l100_m2_e1 | het | 99.3427 | 99.3508 | 99.3346 | 69.0698 | 30759 | 201 | 30752 | 206 | 16 | 7.7670 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.4229 | 96.3710 | 98.4980 | 52.1860 | 30831 | 1161 | 30755 | 469 | 455 | 97.0149 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.0697 | 98.8184 | 99.3222 | 69.4679 | 30775 | 368 | 30774 | 210 | 73 | 34.7619 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.0697 | 98.8184 | 99.3222 | 69.4679 | 30775 | 368 | 30774 | 210 | 73 | 34.7619 | |
| hfeng-pmm3 | SNP | ti | map_l100_m2_e1 | het | 99.5633 | 99.4315 | 99.6955 | 65.7255 | 30784 | 176 | 30777 | 94 | 9 | 9.5745 | |
| dgrover-gatk | SNP | ti | map_l100_m2_e1 | het | 99.4091 | 99.4477 | 99.3705 | 70.9092 | 30789 | 171 | 30782 | 195 | 39 | 20.0000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.5076 | 98.0387 | 98.9810 | 60.6867 | 30792 | 616 | 30792 | 317 | 296 | 93.3754 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.5076 | 98.0387 | 98.9810 | 60.6867 | 30792 | 616 | 30792 | 317 | 296 | 93.3754 | |
| bgallagher-sentieon | SNP | ti | map_l100_m2_e1 | het | 99.2699 | 99.4832 | 99.0575 | 69.3770 | 30800 | 160 | 30793 | 293 | 38 | 12.9693 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.8636 | 96.4960 | 97.2340 | 52.6642 | 30871 | 1121 | 30794 | 876 | 794 | 90.6393 | |
| jpowers-varprowl | SNP | * | map_l150_m2_e0 | * | 97.1685 | 96.6972 | 97.6445 | 80.6949 | 30800 | 1052 | 30800 | 743 | 232 | 31.2248 | |
| eyeh-varpipe | INDEL | D1_5 | HG002complexvar | * | 96.8177 | 96.1241 | 97.5214 | 52.6173 | 31447 | 1268 | 30808 | 783 | 734 | 93.7420 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.5384 | 98.0960 | 98.9848 | 61.0949 | 30810 | 598 | 30810 | 316 | 292 | 92.4051 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.5384 | 98.0960 | 98.9848 | 61.0949 | 30810 | 598 | 30810 | 316 | 292 | 92.4051 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.7392 | 98.1151 | 99.3713 | 57.1912 | 30816 | 592 | 30820 | 195 | 176 | 90.2564 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.7392 | 98.1151 | 99.3713 | 57.1912 | 30816 | 592 | 30820 | 195 | 176 | 90.2564 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.1594 | 97.2539 | 97.0650 | 73.4982 | 29643 | 837 | 30823 | 932 | 445 | 47.7468 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.1594 | 97.2539 | 97.0650 | 73.4982 | 29643 | 837 | 30823 | 932 | 445 | 47.7468 | |
| eyeh-varpipe | SNP | * | map_l150_m2_e0 | * | 98.5884 | 99.6578 | 97.5418 | 78.8388 | 31743 | 109 | 30831 | 777 | 30 | 3.8610 | |
| cchapple-custom | SNP | * | map_l150_m2_e0 | * | 96.6523 | 96.8134 | 96.4917 | 78.8019 | 30837 | 1015 | 30832 | 1121 | 246 | 21.9447 | |
| ghariani-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 92.5410 | 98.7028 | 87.1034 | 79.6250 | 30739 | 404 | 30832 | 4565 | 319 | 6.9880 | |
| ghariani-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 92.5410 | 98.7028 | 87.1034 | 79.6250 | 30739 | 404 | 30832 | 4565 | 319 | 6.9880 | |
| jmaeng-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.0878 | 99.0624 | 99.1133 | 72.7315 | 30851 | 292 | 30851 | 276 | 26 | 9.4203 | |
| jmaeng-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.0878 | 99.0624 | 99.1133 | 72.7315 | 30851 | 292 | 30851 | 276 | 26 | 9.4203 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.0454 | 96.7804 | 99.3438 | 49.5652 | 30962 | 1030 | 30885 | 204 | 187 | 91.6667 | |
| ckim-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.1543 | 99.2037 | 99.1050 | 72.6597 | 30895 | 248 | 30895 | 279 | 24 | 8.6022 | |
| ckim-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.1543 | 99.2037 | 99.1050 | 72.6597 | 30895 | 248 | 30895 | 279 | 24 | 8.6022 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.0631 | 96.8992 | 99.2554 | 50.7827 | 31000 | 992 | 30924 | 232 | 217 | 93.5345 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1042 | 96.9367 | 99.3002 | 49.5751 | 31012 | 980 | 30935 | 218 | 193 | 88.5321 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.1128 | 99.3482 | 98.8786 | 72.9414 | 30940 | 203 | 30949 | 351 | 41 | 11.6809 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.1128 | 99.3482 | 98.8786 | 72.9414 | 30940 | 203 | 30949 | 351 | 41 | 11.6809 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.8203 | 99.3835 | 98.2634 | 72.4925 | 30951 | 192 | 30951 | 547 | 35 | 6.3985 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.8203 | 99.3835 | 98.2634 | 72.4925 | 30951 | 192 | 30951 | 547 | 35 | 6.3985 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 83.3295 | 82.0722 | 84.6259 | 49.0103 | 31107 | 6795 | 30957 | 5624 | 5549 | 98.6664 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.1393 | 96.8242 | 97.4564 | 67.3706 | 30976 | 1016 | 30958 | 808 | 786 | 97.2772 | |