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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
66401-66450 / 86044 show all | |||||||||||||||
| jli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.4114 | 96.3910 | 96.4318 | 79.9786 | 1282 | 48 | 1081 | 40 | 36 | 90.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l125_m1_e0 | * | 98.5857 | 99.1728 | 98.0054 | 86.8862 | 1079 | 9 | 1081 | 22 | 5 | 22.7273 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 97.0857 | 96.0106 | 98.1851 | 47.3483 | 1083 | 45 | 1082 | 20 | 17 | 85.0000 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 94.9783 | 96.9173 | 93.1153 | 84.1668 | 1289 | 41 | 1082 | 80 | 71 | 88.7500 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 86.6071 | 96.2085 | 78.7482 | 40.9794 | 203 | 8 | 1082 | 292 | 279 | 95.5479 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.3205 | 99.5404 | 97.1300 | 67.2155 | 1083 | 5 | 1083 | 32 | 26 | 81.2500 | |
| anovak-vg | INDEL | * | map_l150_m2_e0 | * | 72.9602 | 74.8580 | 71.1564 | 90.5195 | 1054 | 354 | 1083 | 439 | 234 | 53.3030 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.4993 | 99.5404 | 97.4797 | 67.4289 | 1083 | 5 | 1083 | 28 | 22 | 78.5714 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.6339 | 99.5404 | 97.7437 | 66.8858 | 1083 | 5 | 1083 | 25 | 19 | 76.0000 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 50.1059 | 37.3855 | 75.9467 | 75.6447 | 1224 | 2050 | 1083 | 343 | 104 | 30.3207 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.9493 | 99.5404 | 98.3651 | 65.9133 | 1083 | 5 | 1083 | 18 | 16 | 88.8889 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.8600 | 99.6324 | 98.0995 | 67.6806 | 1084 | 4 | 1084 | 21 | 19 | 90.4762 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.7250 | 99.6324 | 97.8339 | 67.7720 | 1084 | 4 | 1084 | 24 | 21 | 87.5000 | |
| gduggal-bwavard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 87.0247 | 88.6166 | 85.4890 | 87.6172 | 1121 | 144 | 1084 | 184 | 65 | 35.3261 | |
| gduggal-snapfb | INDEL | D1_5 | segdup | * | 97.3404 | 97.4615 | 97.2197 | 94.7311 | 1075 | 28 | 1084 | 31 | 5 | 16.1290 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.7250 | 99.6324 | 97.8339 | 67.7720 | 1084 | 4 | 1084 | 24 | 21 | 87.5000 | |
| qzeng-custom | INDEL | I16_PLUS | HG002compoundhet | hetalt | 79.5048 | 66.7941 | 98.1900 | 36.1641 | 1398 | 695 | 1085 | 20 | 16 | 80.0000 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 69.9723 | 87.2727 | 58.3961 | 90.3865 | 1104 | 161 | 1085 | 773 | 47 | 6.0802 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.4241 | 96.8972 | 100.0000 | 48.3349 | 1093 | 35 | 1086 | 0 | 0 | ||
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.1490 | 96.3652 | 100.0000 | 55.8357 | 1087 | 41 | 1086 | 0 | 0 | ||
| gduggal-bwavard | INDEL | D1_5 | map_l125_m2_e0 | * | 92.6484 | 96.6754 | 88.9435 | 89.1467 | 1105 | 38 | 1086 | 135 | 19 | 14.0741 | |
| gduggal-bwavard | INDEL | D1_5 | map_siren | homalt | 97.1880 | 94.7774 | 99.7245 | 70.3593 | 1107 | 61 | 1086 | 3 | 3 | 100.0000 | |
| jpowers-varprowl | INDEL | D1_5 | map_l125_m2_e1 | * | 94.5581 | 93.8634 | 95.2632 | 87.2725 | 1086 | 71 | 1086 | 54 | 28 | 51.8519 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.2295 | 95.0044 | 97.4865 | 79.8699 | 1084 | 57 | 1086 | 28 | 18 | 64.2857 | |
| ltrigg-rtg1 | INDEL | D1_5 | segdup | * | 99.1335 | 98.5494 | 99.7245 | 92.9129 | 1087 | 16 | 1086 | 3 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 93.1414 | 92.1902 | 94.1126 | 70.7669 | 1086 | 92 | 1087 | 68 | 66 | 97.0588 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 77.0774 | 70.4225 | 85.1214 | 55.3497 | 350 | 147 | 1087 | 190 | 150 | 78.9474 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 88.0130 | 91.8782 | 84.4600 | 56.4024 | 1086 | 96 | 1087 | 200 | 133 | 66.5000 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.4743 | 97.4291 | 99.5421 | 56.2675 | 1099 | 29 | 1087 | 5 | 3 | 60.0000 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 41.4402 | 94.0217 | 26.5770 | 81.1312 | 1038 | 66 | 1087 | 3003 | 81 | 2.6973 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 97.8855 | 96.4539 | 99.3601 | 62.1846 | 1088 | 40 | 1087 | 7 | 3 | 42.8571 | |
| gduggal-snapvard | INDEL | I1_5 | map_l125_m2_e0 | * | 90.3981 | 94.5158 | 86.6242 | 88.6067 | 810 | 47 | 1088 | 168 | 70 | 41.6667 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 97.4927 | 96.2865 | 98.7296 | 42.4242 | 1089 | 42 | 1088 | 14 | 12 | 85.7143 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.5329 | 95.0920 | 98.0180 | 79.6517 | 1085 | 56 | 1088 | 22 | 17 | 77.2727 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 77.8419 | 75.4167 | 80.4284 | 80.2278 | 1086 | 354 | 1089 | 265 | 3 | 1.1321 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 97.5369 | 96.2865 | 98.8203 | 42.9016 | 1089 | 42 | 1089 | 13 | 9 | 69.2308 | |
| qzeng-custom | INDEL | D1_5 | segdup | * | 98.3734 | 98.6401 | 98.1081 | 95.0976 | 1088 | 15 | 1089 | 21 | 6 | 28.5714 | |
| eyeh-varpipe | INDEL | D1_5 | map_l100_m0_e0 | * | 97.2110 | 97.1031 | 97.3190 | 85.5164 | 838 | 25 | 1089 | 30 | 15 | 50.0000 | |
| gduggal-bwafb | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 79.7506 | 68.0178 | 96.3749 | 45.6511 | 2601 | 1223 | 1090 | 41 | 40 | 97.5610 | |
| ckim-isaac | INDEL | D16_PLUS | HG002complexvar | * | 76.1289 | 68.2288 | 86.0979 | 58.5597 | 1121 | 522 | 1090 | 176 | 59 | 33.5227 | |
| ltrigg-rtg2 | INDEL | D1_5 | segdup | * | 99.4540 | 99.1840 | 99.7255 | 92.9516 | 1094 | 9 | 1090 | 3 | 0 | 0.0000 | |
| anovak-vg | INDEL | * | map_l100_m1_e0 | homalt | 76.5861 | 87.2046 | 68.2728 | 79.5887 | 1070 | 157 | 1091 | 507 | 474 | 93.4911 | |
| asubramanian-gatk | INDEL | D1_5 | segdup | * | 98.9561 | 98.7307 | 99.1826 | 95.3977 | 1089 | 14 | 1092 | 9 | 1 | 11.1111 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.7166 | 95.4426 | 98.0251 | 79.9026 | 1089 | 52 | 1092 | 22 | 18 | 81.8182 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.1802 | 96.7672 | 99.6350 | 61.0934 | 449 | 15 | 1092 | 4 | 4 | 100.0000 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 97.9702 | 96.0212 | 100.0000 | 40.0000 | 1086 | 45 | 1092 | 0 | 0 | ||
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 90.9557 | 84.7716 | 98.1132 | 33.9074 | 1002 | 180 | 1092 | 21 | 18 | 85.7143 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 47.4332 | 31.5939 | 95.1220 | 44.9136 | 1114 | 2412 | 1092 | 56 | 43 | 76.7857 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 47.4332 | 31.5939 | 95.1220 | 44.9136 | 1114 | 2412 | 1092 | 56 | 43 | 76.7857 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 36.5445 | 33.8941 | 39.6445 | 65.7686 | 1088 | 2122 | 1093 | 1664 | 1651 | 99.2188 | |