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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
49301-49350 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 62.3378 | 47.0343 | 92.4025 | 85.6385 | 452 | 509 | 450 | 37 | 14 | 37.8378 | |
| ckim-isaac | SNP | tv | map_l250_m0_e0 | het | 63.7441 | 47.0280 | 98.8971 | 94.7702 | 269 | 303 | 269 | 3 | 1 | 33.3333 | |
| ckim-gatk | SNP | * | map_l250_m2_e1 | homalt | 63.9640 | 47.0199 | 100.0000 | 93.4676 | 1278 | 1440 | 1278 | 0 | 0 | ||
| gduggal-bwaplat | SNP | ti | map_l125_m0_e0 | * | 63.7993 | 47.0146 | 99.2230 | 91.1459 | 6000 | 6762 | 6002 | 47 | 16 | 34.0426 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 58.9132 | 46.9890 | 78.9474 | 83.7848 | 1662 | 1875 | 1725 | 460 | 86 | 18.6957 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 48.9009 | 46.9867 | 50.9776 | 50.1691 | 15032 | 16960 | 15018 | 14442 | 14205 | 98.3590 | |
| mlin-fermikit | SNP | ti | map_l125_m0_e0 | homalt | 56.8886 | 46.9829 | 72.0875 | 54.0574 | 2110 | 2381 | 2110 | 817 | 761 | 93.1457 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 63.8458 | 46.9811 | 99.5984 | 65.4167 | 249 | 281 | 248 | 1 | 1 | 100.0000 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 60.0475 | 46.9799 | 83.1858 | 54.4355 | 70 | 79 | 94 | 19 | 19 | 100.0000 | |
| jmaeng-gatk | SNP | * | map_l250_m0_e0 | * | 63.1215 | 46.9789 | 96.1649 | 98.1269 | 1003 | 1132 | 1003 | 40 | 3 | 7.5000 | |
| gduggal-bwaplat | INDEL | I1_5 | map_l250_m2_e0 | het | 63.9175 | 46.9697 | 100.0000 | 99.0309 | 31 | 35 | 31 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | I1_5 | map_l250_m2_e1 | het | 63.9175 | 46.9697 | 100.0000 | 99.0657 | 31 | 35 | 31 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | * | map_l100_m2_e1 | hetalt | 63.5897 | 46.9697 | 98.4127 | 95.7461 | 62 | 70 | 62 | 1 | 1 | 100.0000 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 63.6157 | 46.9649 | 98.5586 | 37.4295 | 588 | 664 | 547 | 8 | 6 | 75.0000 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 63.6016 | 46.9512 | 98.5507 | 57.2314 | 77 | 87 | 204 | 3 | 3 | 100.0000 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 57.9068 | 46.9489 | 75.5372 | 67.0120 | 854 | 965 | 914 | 296 | 261 | 88.1757 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 57.9068 | 46.9489 | 75.5372 | 67.0120 | 854 | 965 | 914 | 296 | 261 | 88.1757 | |
| ckim-vqsr | SNP | tv | map_l125_m0_e0 | * | 63.5371 | 46.9462 | 98.2639 | 92.6176 | 3113 | 3518 | 3113 | 55 | 0 | 0.0000 | |
| ckim-gatk | SNP | * | map_l250_m0_e0 | * | 63.1579 | 46.9321 | 96.5318 | 98.1002 | 1002 | 1133 | 1002 | 36 | 2 | 5.5556 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 59.5931 | 46.9320 | 81.6092 | 83.6389 | 283 | 320 | 284 | 64 | 1 | 1.5625 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 49.6345 | 46.9154 | 52.6882 | 51.2725 | 327 | 370 | 343 | 308 | 167 | 54.2208 | |
| jmaeng-gatk | SNP | * | map_l250_m2_e1 | homalt | 63.8458 | 46.9095 | 99.9216 | 93.0622 | 1275 | 1443 | 1275 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | I6_15 | map_siren | * | 63.4176 | 46.8852 | 97.9592 | 84.2105 | 143 | 162 | 144 | 3 | 2 | 66.6667 | |
| ckim-isaac | SNP | * | map_l150_m2_e1 | homalt | 63.8200 | 46.8842 | 99.9099 | 70.9059 | 5545 | 6282 | 5545 | 5 | 5 | 100.0000 | |
| asubramanian-gatk | SNP | * | map_l100_m2_e0 | het | 63.7840 | 46.8782 | 99.7614 | 87.0574 | 21751 | 24648 | 21745 | 52 | 14 | 26.9231 | |
| ckim-isaac | SNP | * | map_l150_m2_e0 | homalt | 63.7998 | 46.8587 | 99.9271 | 70.9027 | 5482 | 6217 | 5482 | 4 | 4 | 100.0000 | |
| anovak-vg | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 46.7905 | 46.8317 | 46.7493 | 53.6445 | 1892 | 2148 | 3092 | 3522 | 2706 | 76.8313 | |
| gduggal-bwaplat | INDEL | * | map_l125_m0_e0 | homalt | 63.7890 | 46.8310 | 100.0000 | 93.6576 | 133 | 151 | 133 | 0 | 0 | ||
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 51.7221 | 46.8234 | 57.7656 | 39.6200 | 17747 | 20155 | 24726 | 18078 | 14175 | 78.4102 | |
| mlin-fermikit | INDEL | I1_5 | map_l150_m2_e0 | * | 61.4412 | 46.8208 | 89.3382 | 85.2734 | 243 | 276 | 243 | 29 | 25 | 86.2069 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m1_e0 | hetalt | 63.7681 | 46.8085 | 100.0000 | 89.1089 | 22 | 25 | 22 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 62.8571 | 46.8085 | 95.6522 | 83.6879 | 22 | 25 | 22 | 1 | 1 | 100.0000 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 45.3594 | 46.8085 | 43.9974 | 84.7177 | 638 | 725 | 667 | 849 | 19 | 2.2379 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 63.4096 | 46.8051 | 98.2726 | 36.6180 | 586 | 666 | 512 | 9 | 6 | 66.6667 | |
| ckim-gatk | SNP | * | map_l250_m2_e0 | homalt | 63.7586 | 46.7982 | 100.0000 | 93.4789 | 1257 | 1429 | 1257 | 0 | 0 | ||
| egarrison-hhga | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 63.4351 | 46.7851 | 98.4838 | 42.8226 | 3187 | 3625 | 2793 | 43 | 38 | 88.3721 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 59.0350 | 46.7546 | 80.0643 | 63.0729 | 1311 | 1493 | 1245 | 310 | 228 | 73.5484 | |
| ckim-isaac | SNP | tv | map_l250_m2_e1 | het | 63.5294 | 46.7176 | 99.2432 | 92.2217 | 918 | 1047 | 918 | 7 | 1 | 14.2857 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 0.0000 | 46.7074 | 0.0000 | 0.0000 | 7802 | 8902 | 0 | 0 | 0 | ||
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 0.0000 | 46.7074 | 0.0000 | 0.0000 | 7802 | 8902 | 0 | 0 | 0 | ||
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 62.7608 | 46.6890 | 95.7058 | 37.3301 | 2228 | 2544 | 2251 | 101 | 89 | 88.1188 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 63.3251 | 46.6890 | 98.3795 | 37.6873 | 2228 | 2544 | 1882 | 31 | 28 | 90.3226 | |
| jmaeng-gatk | SNP | * | map_l250_m2_e0 | homalt | 63.6387 | 46.6865 | 99.9203 | 93.0743 | 1254 | 1432 | 1254 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | SNP | tv | map_l125_m1_e0 | homalt | 63.6417 | 46.6724 | 100.0000 | 80.2470 | 2735 | 3125 | 2735 | 0 | 0 | ||
| gduggal-bwaplat | SNP | ti | map_l150_m1_e0 | hetalt | 63.6364 | 46.6667 | 100.0000 | 92.4731 | 7 | 8 | 7 | 0 | 0 | ||
| gduggal-bwaplat | SNP | ti | map_l150_m2_e0 | hetalt | 63.6364 | 46.6667 | 100.0000 | 93.7500 | 7 | 8 | 7 | 0 | 0 | ||
| gduggal-bwaplat | SNP | ti | map_l150_m2_e1 | hetalt | 63.6364 | 46.6667 | 100.0000 | 93.8053 | 7 | 8 | 7 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | D1_5 | map_l250_m2_e0 | homalt | 63.6364 | 46.6667 | 100.0000 | 97.3783 | 28 | 32 | 28 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | D1_5 | map_l250_m2_e1 | homalt | 63.6364 | 46.6667 | 100.0000 | 97.4476 | 28 | 32 | 28 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | I6_15 | map_l125_m1_e0 | homalt | 63.6364 | 46.6667 | 100.0000 | 94.1176 | 7 | 8 | 7 | 0 | 0 | ||