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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
6551-6600 / 86044 show all | |||||||||||||||
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 53.2289 | 38.9258 | 84.1491 | 87.7362 | 1464 | 2297 | 1513 | 285 | 71 | 24.9123 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 69.6060 | 94.2197 | 55.1887 | 74.6108 | 326 | 20 | 351 | 285 | 24 | 8.4211 | |
| eyeh-varpipe | INDEL | * | HG002complexvar | hetalt | 61.1209 | 45.5799 | 92.7426 | 76.1697 | 1686 | 2013 | 3642 | 285 | 277 | 97.1930 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 84.2828 | 78.0622 | 91.5805 | 48.9211 | 3110 | 874 | 3100 | 285 | 235 | 82.4561 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 84.2729 | 74.8150 | 96.4680 | 58.6163 | 7786 | 2621 | 7784 | 285 | 97 | 34.0351 | |
| gduggal-bwaplat | INDEL | I1_5 | HG002complexvar | * | 92.5060 | 86.7938 | 99.0230 | 59.4097 | 28957 | 4406 | 28886 | 285 | 203 | 71.2281 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 44.5283 | 92.9134 | 29.2804 | 23.5294 | 118 | 9 | 118 | 285 | 276 | 96.8421 | |
| hfeng-pmm2 | SNP | * | map_l150_m2_e0 | * | 99.2475 | 99.3878 | 99.1076 | 77.7218 | 31657 | 195 | 31651 | 285 | 34 | 11.9298 | |
| hfeng-pmm3 | INDEL | * | HG002compoundhet | het | 86.9738 | 82.7064 | 91.7055 | 77.8323 | 3386 | 708 | 3151 | 285 | 268 | 94.0351 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 31.8686 | 65.5405 | 21.0526 | 51.2162 | 97 | 51 | 76 | 285 | 285 | 100.0000 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 75.7234 | 65.8935 | 89.0004 | 54.7661 | 2301 | 1191 | 2306 | 285 | 284 | 99.6491 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 75.3565 | 68.2801 | 84.0693 | 69.0324 | 1453 | 675 | 1504 | 285 | 237 | 83.1579 | |
| qzeng-custom | SNP | tv | map_l125_m2_e1 | het | 85.6436 | 76.9070 | 96.6195 | 86.8249 | 8116 | 2437 | 8117 | 284 | 231 | 81.3380 | |
| gduggal-snapvard | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | het | 29.4957 | 83.3333 | 17.9191 | 92.6664 | 55 | 11 | 62 | 284 | 5 | 1.7606 | |
| anovak-vg | INDEL | I16_PLUS | HG002complexvar | * | 33.1975 | 24.5225 | 51.3699 | 42.4631 | 321 | 988 | 300 | 284 | 225 | 79.2254 | |
| ciseli-custom | INDEL | I1_5 | map_l100_m1_e0 | het | 69.4206 | 72.4582 | 66.6275 | 85.4704 | 563 | 214 | 567 | 284 | 245 | 86.2676 | |
| ckim-gatk | SNP | ti | segdup | het | 98.6041 | 99.5428 | 97.6830 | 94.4043 | 11975 | 55 | 11973 | 284 | 5 | 1.7606 | |
| jpowers-varprowl | INDEL | D16_PLUS | HG002complexvar | * | 75.6960 | 71.3329 | 80.6276 | 65.0203 | 1172 | 471 | 1182 | 284 | 273 | 96.1268 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.8814 | 97.0742 | 98.7022 | 53.8225 | 21599 | 651 | 21600 | 284 | 276 | 97.1831 | |
| rpoplin-dv42 | INDEL | I1_5 | HG002compoundhet | het | 81.6272 | 92.2353 | 73.2075 | 84.1151 | 784 | 66 | 776 | 284 | 279 | 98.2394 | |
| ckim-vqsr | SNP | * | map_l125_m2_e1 | * | 70.6297 | 54.9235 | 98.9163 | 88.7326 | 25925 | 21277 | 25922 | 284 | 6 | 2.1127 | |
| ckim-vqsr | SNP | * | map_l125_m2_e0 | * | 70.4819 | 54.7482 | 98.9056 | 88.7400 | 25580 | 21143 | 25577 | 283 | 6 | 2.1201 | |
| jli-custom | SNP | * | map_l100_m2_e1 | * | 99.4761 | 99.3323 | 99.6202 | 63.1271 | 74238 | 499 | 74235 | 283 | 79 | 27.9152 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.1514 | 97.5955 | 98.7136 | 53.8931 | 21715 | 535 | 21716 | 283 | 267 | 94.3463 | |
| asubramanian-gatk | SNP | * | HG002compoundhet | * | 97.7516 | 96.6501 | 98.8785 | 41.8929 | 24957 | 865 | 24950 | 283 | 28 | 9.8940 | |
| qzeng-custom | SNP | tv | map_l125_m2_e0 | het | 85.5513 | 76.7765 | 96.5908 | 86.8303 | 8017 | 2425 | 8018 | 283 | 230 | 81.2721 | |
| qzeng-custom | SNP | tv | map_l150_m2_e0 | * | 82.9982 | 72.7081 | 96.6811 | 87.1519 | 8256 | 3099 | 8244 | 283 | 238 | 84.0989 | |
| gduggal-snapvard | SNP | tv | * | homalt | 99.4119 | 98.9054 | 99.9237 | 19.2463 | 372995 | 4128 | 370593 | 283 | 154 | 54.4170 | |
| gduggal-snapplat | INDEL | * | map_l100_m1_e0 | het | 79.4811 | 73.6018 | 86.3811 | 92.1058 | 1645 | 590 | 1795 | 283 | 31 | 10.9541 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 49.2494 | 39.3734 | 65.7385 | 28.0488 | 465 | 716 | 543 | 283 | 280 | 98.9399 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 45.3517 | 52.2843 | 40.0424 | 58.1189 | 103 | 94 | 189 | 283 | 245 | 86.5724 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.2261 | 96.1390 | 98.3380 | 67.3449 | 17131 | 688 | 16745 | 283 | 223 | 78.7986 | |
| ckim-dragen | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.0870 | 99.1898 | 97.0085 | 80.9382 | 9059 | 74 | 9177 | 283 | 13 | 4.5936 | |
| ckim-dragen | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.0870 | 99.1898 | 97.0085 | 80.9382 | 9059 | 74 | 9177 | 283 | 13 | 4.5936 | |
| cchapple-custom | SNP | * | map_l250_m2_e1 | * | 96.1831 | 95.9309 | 96.4367 | 90.2654 | 7662 | 325 | 7659 | 283 | 66 | 23.3216 | |
| rpoplin-dv42 | SNP | tv | * | het | 99.9398 | 99.9275 | 99.9522 | 22.4174 | 591267 | 429 | 591187 | 283 | 104 | 36.7491 | |
| hfeng-pmm2 | SNP | * | map_l100_m0_e0 | * | 99.2701 | 99.4001 | 99.1404 | 70.5461 | 32644 | 197 | 32640 | 283 | 34 | 12.0141 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.5612 | 98.0245 | 99.1037 | 50.2646 | 31360 | 632 | 31292 | 283 | 258 | 91.1661 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 30.5547 | 21.2500 | 54.3548 | 46.8723 | 102 | 378 | 337 | 283 | 282 | 99.6466 | |
| gduggal-bwavard | INDEL | C1_5 | HG002complexvar | het | 82.2319 | 85.7143 | 79.0215 | 80.8462 | 6 | 1 | 1066 | 283 | 105 | 37.1025 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 80.6675 | 73.6706 | 89.1329 | 45.4946 | 7717 | 2758 | 2313 | 282 | 188 | 66.6667 | |
| gduggal-bwafb | SNP | * | map_l125_m0_e0 | het | 98.0108 | 98.2391 | 97.7835 | 78.4484 | 12441 | 223 | 12441 | 282 | 70 | 24.8227 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 77.6372 | 81.0471 | 74.5027 | 77.6881 | 774 | 181 | 824 | 282 | 193 | 68.4397 | |
| gduggal-snapplat | SNP | tv | HG002complexvar | homalt | 98.5607 | 97.4503 | 99.6966 | 24.7080 | 92686 | 2425 | 92657 | 282 | 135 | 47.8723 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 59.9388 | 63.0225 | 57.1429 | 46.3295 | 196 | 115 | 376 | 282 | 235 | 83.3333 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 94.7617 | 96.8094 | 92.7988 | 67.6203 | 3641 | 120 | 3634 | 282 | 273 | 96.8085 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 94.7617 | 96.8094 | 92.7988 | 67.6203 | 3641 | 120 | 3634 | 282 | 273 | 96.8085 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 57.8720 | 92.5676 | 42.0945 | 50.6085 | 137 | 11 | 205 | 282 | 275 | 97.5177 | |
| jlack-gatk | INDEL | * | map_l100_m2_e1 | * | 95.3410 | 97.9233 | 92.8914 | 88.4293 | 3678 | 78 | 3685 | 282 | 30 | 10.6383 | |
| cchapple-custom | SNP | * | map_l250_m2_e1 | het | 95.2117 | 95.7257 | 94.7032 | 91.6862 | 5039 | 225 | 5042 | 282 | 65 | 23.0496 | |