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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
67001-67050 / 86044 show all | |||||||||||||||
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 93.7394 | 94.9841 | 92.5270 | 73.6767 | 1193 | 63 | 1201 | 97 | 62 | 63.9175 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 83.6630 | 95.0637 | 74.7040 | 77.8987 | 1194 | 62 | 1199 | 406 | 377 | 92.8571 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 22.0793 | 12.5407 | 92.2309 | 57.4591 | 1194 | 8327 | 1294 | 109 | 93 | 85.3211 | |
| jmaeng-gatk | INDEL | D1_5 | map_l100_m1_e0 | het | 96.0274 | 98.7593 | 93.4426 | 89.0578 | 1194 | 15 | 1197 | 84 | 6 | 7.1429 | |
| jli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.9085 | 96.9156 | 98.9221 | 57.0053 | 1194 | 38 | 1193 | 13 | 11 | 84.6154 | |
| jli-custom | INDEL | D1_5 | map_l100_m1_e0 | het | 98.6387 | 98.8420 | 98.4362 | 81.9143 | 1195 | 14 | 1196 | 19 | 5 | 26.3158 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 86.2568 | 87.6742 | 84.8845 | 71.5339 | 1195 | 168 | 1213 | 216 | 204 | 94.4444 | |
| cchapple-custom | INDEL | * | map_l100_m1_e0 | homalt | 98.1520 | 97.3920 | 98.9238 | 81.1132 | 1195 | 32 | 1195 | 13 | 9 | 69.2308 | |
| qzeng-custom | INDEL | D1_5 | HG002complexvar | hetalt | 93.1197 | 88.3876 | 98.3871 | 70.2875 | 1195 | 157 | 183 | 3 | 3 | 100.0000 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 78.4884 | 95.1433 | 66.7958 | 80.7253 | 1195 | 61 | 1207 | 600 | 372 | 62.0000 | |
| gduggal-bwaplat | SNP | ti | map_l250_m1_e0 | het | 57.3348 | 40.2965 | 99.3367 | 97.5609 | 1196 | 1772 | 1198 | 8 | 2 | 25.0000 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m1_e0 | het | 92.3518 | 98.9247 | 86.5979 | 88.3812 | 1196 | 13 | 1176 | 182 | 48 | 26.3736 | |
| cchapple-custom | INDEL | D1_5 | HG002complexvar | hetalt | 0.0000 | 88.4615 | 0.0000 | 0.0000 | 1196 | 156 | 0 | 0 | 0 | ||
| ciseli-custom | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 35.0447 | 30.4403 | 41.2903 | 53.1797 | 1196 | 2733 | 1216 | 1729 | 1499 | 86.6975 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 93.3273 | 88.3962 | 98.8411 | 66.0101 | 1196 | 157 | 1194 | 14 | 3 | 21.4286 | |
| astatham-gatk | INDEL | D1_5 | map_l100_m2_e1 | het | 95.9899 | 94.3218 | 97.7180 | 85.7871 | 1196 | 72 | 1199 | 28 | 4 | 14.2857 | |
| mlin-fermikit | INDEL | * | map_l125_m1_e0 | * | 68.2325 | 56.7632 | 85.5103 | 80.5660 | 1196 | 911 | 1198 | 203 | 159 | 78.3251 | |
| ltrigg-rtg2 | INDEL | I6_15 | HG002complexvar | homalt | 98.9542 | 98.5173 | 99.3950 | 43.5610 | 1196 | 18 | 1150 | 7 | 4 | 57.1429 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m1_e0 | het | 98.6818 | 98.9247 | 98.4401 | 85.0991 | 1196 | 13 | 1199 | 19 | 3 | 15.7895 | |
| gduggal-snapfb | INDEL | I1_5 | map_siren | homalt | 98.0751 | 98.6799 | 97.4776 | 83.6569 | 1196 | 16 | 1198 | 31 | 13 | 41.9355 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m1_e0 | het | 91.4439 | 99.0074 | 84.9539 | 88.4423 | 1197 | 12 | 1197 | 212 | 63 | 29.7170 | |
| jlack-gatk | INDEL | D1_5 | map_l100_m1_e0 | het | 93.4933 | 99.0074 | 88.5609 | 87.9481 | 1197 | 12 | 1200 | 155 | 10 | 6.4516 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 93.9929 | 92.3611 | 95.6835 | 84.8474 | 1197 | 99 | 1197 | 54 | 26 | 48.1481 | |
| asubramanian-gatk | INDEL | * | map_l100_m2_e1 | homalt | 96.3001 | 93.4426 | 99.3377 | 85.6787 | 1197 | 84 | 1200 | 8 | 3 | 37.5000 | |
| qzeng-custom | INDEL | I6_15 | HG002complexvar | homalt | 93.7520 | 98.5997 | 89.3586 | 51.1570 | 1197 | 17 | 1226 | 146 | 83 | 56.8493 | |
| ltrigg-rtg1 | INDEL | I6_15 | HG002complexvar | homalt | 98.9952 | 98.6820 | 99.3103 | 43.9072 | 1198 | 16 | 1152 | 8 | 5 | 62.5000 | |
| gduggal-snapfb | INDEL | * | map_l100_m2_e0 | homalt | 96.6525 | 95.0040 | 98.3593 | 87.2369 | 1198 | 63 | 1199 | 20 | 12 | 60.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.9954 | 97.2403 | 98.7624 | 61.1289 | 1198 | 34 | 1197 | 15 | 13 | 86.6667 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l100_m1_e0 | het | 99.0096 | 99.0902 | 98.9292 | 80.5480 | 1198 | 11 | 1201 | 13 | 2 | 15.3846 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l100_m1_e0 | het | 98.4026 | 99.1729 | 97.6442 | 83.5954 | 1199 | 10 | 1202 | 29 | 2 | 6.8966 | |
| ltrigg-rtg2 | INDEL | * | map_l100_m1_e0 | homalt | 98.6835 | 97.7180 | 99.6683 | 77.1071 | 1199 | 28 | 1202 | 4 | 2 | 50.0000 | |
| jpowers-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 89.1155 | 94.7826 | 84.0878 | 89.9821 | 1199 | 66 | 1226 | 232 | 79 | 34.0517 | |
| ckim-dragen | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 98.8879 | 97.9575 | 99.8361 | 58.2906 | 1199 | 25 | 1218 | 2 | 2 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | map_l100_m1_e0 | het | 96.0438 | 99.1729 | 93.1061 | 88.7944 | 1199 | 10 | 1202 | 89 | 6 | 6.7416 | |
| cchapple-custom | INDEL | I1_5 | map_siren | homalt | 99.3361 | 98.9274 | 99.7481 | 76.2512 | 1199 | 13 | 1188 | 3 | 2 | 66.6667 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 98.0772 | 97.3214 | 98.8449 | 61.2532 | 1199 | 33 | 1198 | 14 | 12 | 85.7143 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 98.0772 | 97.3214 | 98.8449 | 61.5726 | 1199 | 33 | 1198 | 14 | 12 | 85.7143 | |
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 95.5795 | 91.5332 | 100.0000 | 25.9259 | 1200 | 111 | 1200 | 0 | 0 | ||
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 91.8474 | 91.0470 | 92.6620 | 63.5458 | 1200 | 118 | 1187 | 94 | 90 | 95.7447 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 88.8820 | 96.0769 | 82.6897 | 71.8992 | 1200 | 49 | 1199 | 251 | 105 | 41.8327 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 88.8820 | 96.0769 | 82.6897 | 71.8992 | 1200 | 49 | 1199 | 251 | 105 | 41.8327 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 84.7915 | 95.5414 | 76.2159 | 71.9574 | 1200 | 56 | 1426 | 445 | 60 | 13.4831 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 98.9695 | 98.0392 | 99.9176 | 57.2234 | 1200 | 24 | 1213 | 1 | 1 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 98.1189 | 97.4026 | 98.8458 | 61.2336 | 1200 | 32 | 1199 | 14 | 12 | 85.7143 | |
| gduggal-bwafb | INDEL | I1_5 | map_siren | homalt | 98.9302 | 99.0099 | 98.8506 | 78.8211 | 1200 | 12 | 1204 | 14 | 8 | 57.1429 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l100_m1_e0 | het | 98.5653 | 99.2556 | 97.8845 | 84.2173 | 1200 | 9 | 1203 | 26 | 4 | 15.3846 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.4659 | 95.6210 | 97.3258 | 79.6370 | 1201 | 55 | 1201 | 33 | 10 | 30.3030 | |
| ckim-vqsr | INDEL | D1_5 | HG002complexvar | hetalt | 92.5788 | 88.8314 | 96.6563 | 72.4212 | 1201 | 151 | 1243 | 43 | 43 | 100.0000 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 61.9377 | 88.6347 | 47.6003 | 71.2150 | 1201 | 154 | 1210 | 1332 | 1313 | 98.5736 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 59.8779 | 85.1773 | 46.1658 | 67.0074 | 1201 | 209 | 1192 | 1390 | 1248 | 89.7842 | |