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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
78551-78600 / 86044 show all | |||||||||||||||
| raldana-dualsentieon | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.1260 | 92.3762 | 93.8881 | 76.4157 | 3732 | 308 | 3441 | 224 | 202 | 90.1786 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.7222 | 98.4748 | 98.9709 | 68.2697 | 21565 | 334 | 21542 | 224 | 207 | 92.4107 | |
| ndellapenna-hhga | INDEL | * | * | hetalt | 84.9841 | 74.5730 | 98.7738 | 62.9843 | 18820 | 6417 | 18044 | 224 | 192 | 85.7143 | |
| ltrigg-rtg2 | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.1654 | 99.5545 | 98.7794 | 37.2444 | 18102 | 81 | 18127 | 224 | 7 | 3.1250 | |
| jlack-gatk | INDEL | I16_PLUS | * | * | 95.3468 | 94.3077 | 96.4091 | 70.3461 | 6014 | 363 | 6014 | 224 | 155 | 69.1964 | |
| gduggal-bwavard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 86.3919 | 88.4669 | 84.4120 | 88.2444 | 1258 | 164 | 1213 | 224 | 72 | 32.1429 | |
| gduggal-bwafb | SNP | ti | map_l150_m2_e0 | het | 98.3596 | 98.4551 | 98.2644 | 79.4915 | 12682 | 199 | 12682 | 224 | 63 | 28.1250 | |
| gduggal-bwafb | SNP | ti | map_l150_m1_e0 | * | 98.7276 | 98.5998 | 98.8556 | 76.3349 | 19436 | 276 | 19436 | 225 | 69 | 30.6667 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 31.2539 | 22.7545 | 49.8886 | 70.3042 | 228 | 774 | 224 | 225 | 200 | 88.8889 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 59.7518 | 76.0417 | 49.2099 | 69.9253 | 219 | 69 | 218 | 225 | 200 | 88.8889 | |
| ciseli-custom | INDEL | I1_5 | map_l125_m2_e1 | * | 59.4882 | 53.3333 | 67.2489 | 88.9869 | 464 | 406 | 462 | 225 | 194 | 86.2222 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.3986 | 91.8696 | 99.2095 | 63.6282 | 28260 | 2501 | 28237 | 225 | 152 | 67.5556 | |
| ckim-dragen | INDEL | D16_PLUS | * | * | 97.1268 | 97.5531 | 96.7043 | 72.5515 | 6618 | 166 | 6602 | 225 | 138 | 61.3333 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.4476 | 97.2827 | 97.6130 | 45.1498 | 9201 | 257 | 9201 | 225 | 220 | 97.7778 | |
| bgallagher-sentieon | SNP | ti | map_l125_m2_e1 | het | 99.0933 | 99.3608 | 98.8273 | 75.6520 | 18965 | 122 | 18961 | 225 | 33 | 14.6667 | |
| anovak-vg | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 96.0247 | 96.7157 | 95.3435 | 43.9443 | 4535 | 154 | 4607 | 225 | 89 | 39.5556 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 66.6828 | 57.1125 | 80.1061 | 51.0601 | 538 | 404 | 906 | 225 | 212 | 94.2222 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 83.6293 | 78.9187 | 88.9381 | 47.0175 | 3766 | 1006 | 1809 | 225 | 103 | 45.7778 | |
| gduggal-snapvard | INDEL | D1_5 | map_l150_m1_e0 | het | 83.7248 | 98.3402 | 72.8916 | 90.7572 | 474 | 8 | 605 | 225 | 50 | 22.2222 | |
| ghariani-varprowl | INDEL | * | map_l125_m1_e0 | het | 91.1754 | 97.9026 | 85.3133 | 91.4837 | 1307 | 28 | 1307 | 225 | 73 | 32.4444 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m1_e0 | * | 91.4375 | 94.4805 | 88.5845 | 86.5571 | 1746 | 102 | 1746 | 225 | 65 | 28.8889 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 85.9953 | 87.2932 | 84.7354 | 73.4127 | 1161 | 169 | 1249 | 225 | 212 | 94.2222 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 95.4186 | 95.3591 | 95.4783 | 74.6523 | 4767 | 232 | 4751 | 225 | 163 | 72.4444 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 95.4186 | 95.3591 | 95.4783 | 74.6523 | 4767 | 232 | 4751 | 225 | 163 | 72.4444 | |
| hfeng-pmm2 | INDEL | I1_5 | HG002compoundhet | * | 96.1838 | 94.3347 | 98.1069 | 65.2150 | 11656 | 700 | 11660 | 225 | 222 | 98.6667 | |
| jpowers-varprowl | SNP | ti | map_l150_m0_e0 | het | 94.9778 | 94.4281 | 95.5339 | 85.9705 | 4813 | 284 | 4813 | 225 | 82 | 36.4444 | |
| mlin-fermikit | INDEL | * | map_l100_m2_e0 | homalt | 77.0808 | 73.9096 | 80.5363 | 81.0585 | 932 | 329 | 931 | 225 | 197 | 87.5556 | |
| ndellapenna-hhga | INDEL | D1_5 | HG002complexvar | homalt | 98.4078 | 98.9338 | 97.8875 | 56.5863 | 10485 | 113 | 10472 | 226 | 169 | 74.7788 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.9082 | 98.0492 | 93.8587 | 69.1405 | 3468 | 69 | 3454 | 226 | 220 | 97.3451 | |
| ckim-dragen | SNP | * | map_l250_m2_e0 | het | 96.3481 | 96.9965 | 95.7083 | 91.3532 | 5038 | 156 | 5040 | 226 | 15 | 6.6372 | |
| gduggal-bwafb | SNP | ti | map_l150_m2_e1 | het | 98.3690 | 98.4710 | 98.2671 | 79.5893 | 12816 | 199 | 12816 | 226 | 64 | 28.3186 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 67.3062 | 52.6056 | 93.4092 | 74.8938 | 3200 | 2883 | 3203 | 226 | 95 | 42.0354 | |
| raldana-dualsentieon | SNP | ti | map_l150_m2_e1 | het | 98.4895 | 98.7092 | 98.2707 | 77.9738 | 12847 | 168 | 12843 | 226 | 3 | 1.3274 | |
| bgallagher-sentieon | SNP | * | segdup | het | 99.2648 | 99.8268 | 98.7091 | 91.1291 | 17287 | 30 | 17281 | 226 | 2 | 0.8850 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.3409 | 95.9881 | 98.7323 | 65.6784 | 15432 | 645 | 17602 | 226 | 202 | 89.3805 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.3409 | 95.9881 | 98.7323 | 65.6784 | 15432 | 645 | 17602 | 226 | 202 | 89.3805 | |
| anovak-vg | INDEL | D1_5 | map_l125_m2_e1 | * | 83.4613 | 85.4797 | 81.5359 | 87.6226 | 989 | 168 | 998 | 226 | 83 | 36.7257 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 90.2679 | 97.6311 | 83.9375 | 60.3774 | 1154 | 28 | 1181 | 226 | 172 | 76.1062 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 95.8792 | 96.9561 | 94.8260 | 86.0126 | 4109 | 129 | 4142 | 226 | 11 | 4.8673 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.5535 | 97.1688 | 93.9910 | 58.3407 | 3535 | 103 | 3535 | 226 | 68 | 30.0885 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.7577 | 99.3291 | 98.1927 | 66.2045 | 12437 | 84 | 12279 | 226 | 215 | 95.1327 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.4366 | 98.2863 | 98.5874 | 60.3465 | 15772 | 275 | 15773 | 226 | 212 | 93.8053 | |
| hfeng-pmm2 | INDEL | I6_15 | * | homalt | 98.0364 | 99.6314 | 96.4918 | 51.1007 | 6216 | 23 | 6216 | 226 | 223 | 98.6726 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.1834 | 97.9681 | 98.3997 | 62.7279 | 14320 | 297 | 13958 | 227 | 196 | 86.3436 | |
| ciseli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 94.8802 | 99.4227 | 90.7347 | 62.0390 | 2239 | 13 | 2223 | 227 | 39 | 17.1806 | |
| ciseli-custom | INDEL | * | map_l150_m2_e0 | het | 66.9093 | 62.8035 | 71.5895 | 93.6451 | 569 | 337 | 572 | 227 | 132 | 58.1498 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 72.9938 | 64.5494 | 83.9802 | 62.7497 | 1189 | 653 | 1190 | 227 | 214 | 94.2731 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 53.8085 | 55.7377 | 52.0085 | 38.7306 | 68 | 54 | 246 | 227 | 226 | 99.5595 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.7214 | 99.2652 | 98.1834 | 66.0056 | 12429 | 92 | 12269 | 227 | 213 | 93.8326 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.2939 | 98.0121 | 98.5773 | 60.5225 | 15728 | 319 | 15729 | 227 | 215 | 94.7137 | |