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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
9051-9100 / 86044 show all | |||||||||||||||
| bgallagher-sentieon | SNP | * | map_l100_m2_e1 | het | 99.2207 | 99.5181 | 98.9251 | 70.1134 | 46672 | 226 | 46661 | 507 | 63 | 12.4260 | |
| anovak-vg | INDEL | * | map_l250_m2_e0 | * | 67.7533 | 69.7885 | 65.8333 | 96.4399 | 231 | 100 | 237 | 123 | 63 | 51.2195 | |
| anovak-vg | INDEL | * | map_l250_m2_e1 | * | 67.7462 | 69.9700 | 65.6593 | 96.4861 | 233 | 100 | 239 | 125 | 63 | 50.4000 | |
| anovak-vg | INDEL | D1_5 | map_l150_m2_e0 | * | 82.1745 | 84.1415 | 80.2974 | 90.0210 | 642 | 121 | 648 | 159 | 63 | 39.6226 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 23.2825 | 16.1074 | 41.9847 | 51.3011 | 24 | 125 | 55 | 76 | 63 | 82.8947 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 96.3287 | 96.4131 | 96.2444 | 58.5642 | 3790 | 141 | 3844 | 150 | 63 | 42.0000 | |
| astatham-gatk | INDEL | * | HG002complexvar | hetalt | 96.3890 | 94.5391 | 98.3127 | 68.6296 | 3497 | 202 | 3729 | 64 | 63 | 98.4375 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 94.6615 | 98.9726 | 90.7104 | 82.2631 | 867 | 9 | 664 | 68 | 63 | 92.6471 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.8111 | 95.6479 | 98.0030 | 65.9757 | 3890 | 177 | 3877 | 79 | 63 | 79.7468 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1325 | 96.6975 | 99.6107 | 39.2966 | 17656 | 603 | 17657 | 69 | 63 | 91.3043 | |
| hfeng-pmm3 | INDEL | D16_PLUS | HG002compoundhet | * | 95.0927 | 93.1226 | 97.1480 | 33.6879 | 2180 | 161 | 2180 | 64 | 63 | 98.4375 | |
| hfeng-pmm2 | INDEL | D16_PLUS | HG002compoundhet | * | 95.1177 | 93.2080 | 97.1073 | 33.8339 | 2182 | 159 | 2182 | 65 | 63 | 96.9231 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.9618 | 99.7173 | 98.2178 | 72.3769 | 3527 | 10 | 3527 | 64 | 63 | 98.4375 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 90.6706 | 100.0000 | 82.9333 | 68.7239 | 311 | 0 | 311 | 64 | 63 | 98.4375 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.5215 | 99.3655 | 97.6917 | 75.5520 | 45412 | 290 | 45412 | 1073 | 63 | 5.8714 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.5215 | 99.3655 | 97.6917 | 75.5520 | 45412 | 290 | 45412 | 1073 | 63 | 5.8714 | |
| ckim-dragen | SNP | ti | map_l125_m1_e0 | het | 97.7308 | 99.0200 | 96.4747 | 76.6075 | 18087 | 179 | 18089 | 661 | 63 | 9.5310 | |
| ckim-gatk | INDEL | * | HG002complexvar | hetalt | 91.5474 | 85.7529 | 98.1818 | 66.4439 | 3172 | 527 | 3402 | 63 | 63 | 100.0000 | |
| ciseli-custom | INDEL | D1_5 | map_l100_m0_e0 | * | 77.3981 | 72.8853 | 82.5065 | 89.4982 | 629 | 234 | 632 | 134 | 63 | 47.0149 | |
| ciseli-custom | INDEL | I1_5 | map_l125_m0_e0 | het | 62.2449 | 63.5417 | 61.0000 | 91.6771 | 122 | 70 | 122 | 78 | 63 | 80.7692 | |
| ckim-dragen | INDEL | * | HG002complexvar | hetalt | 95.4523 | 92.7548 | 98.3114 | 67.8279 | 3431 | 268 | 3668 | 63 | 63 | 100.0000 | |
| gduggal-snapvard | INDEL | I1_5 | map_l125_m1_e0 | het | 88.6113 | 98.7654 | 80.3504 | 90.3081 | 480 | 6 | 642 | 157 | 63 | 40.1274 | |
| gduggal-snapvard | SNP | ti | HG002compoundhet | homalt | 89.4254 | 81.9989 | 98.3311 | 34.6481 | 6063 | 1331 | 5067 | 86 | 63 | 73.2558 | |
| 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 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m2_e0 | het | 91.5991 | 98.9650 | 85.2538 | 88.9688 | 1243 | 13 | 1243 | 215 | 63 | 29.3023 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 42.7404 | 30.1771 | 73.2258 | 61.7378 | 1176 | 2721 | 1135 | 415 | 63 | 15.1807 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 85.8383 | 78.3200 | 94.9533 | 28.7854 | 6340 | 1755 | 2032 | 108 | 63 | 58.3333 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 67.5325 | 67.7083 | 67.3575 | 24.9027 | 130 | 62 | 130 | 63 | 63 | 100.0000 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 86.2429 | 82.3474 | 90.5252 | 56.5548 | 877 | 188 | 879 | 92 | 63 | 68.4783 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 65.1163 | 73.2026 | 58.6387 | 74.4652 | 112 | 41 | 112 | 79 | 62 | 78.4810 | |
| ghariani-varprowl | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.4684 | 99.6391 | 97.3249 | 58.7610 | 17115 | 62 | 17136 | 471 | 62 | 13.1635 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.5421 | 99.6910 | 99.3935 | 43.8031 | 10325 | 32 | 10325 | 63 | 62 | 98.4127 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 30.0306 | 17.9045 | 93.0510 | 37.7282 | 851 | 3902 | 857 | 64 | 62 | 96.8750 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 63.1130 | 55.0847 | 73.8806 | 56.5640 | 195 | 159 | 198 | 70 | 62 | 88.5714 | |
| gduggal-snapvard | SNP | tv | map_l125_m0_e0 | * | 89.3998 | 96.0489 | 83.6117 | 82.4411 | 6369 | 262 | 6357 | 1246 | 62 | 4.9759 | |
| rpoplin-dv42 | INDEL | D6_15 | HG002complexvar | het | 97.7459 | 97.7564 | 97.7354 | 59.1947 | 3050 | 70 | 3021 | 70 | 62 | 88.5714 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.6672 | 99.9578 | 97.4095 | 54.3286 | 2369 | 1 | 2369 | 63 | 62 | 98.4127 | |
| qzeng-custom | INDEL | D1_5 | HG002complexvar | homalt | 99.0114 | 98.8205 | 99.2030 | 52.6484 | 10473 | 125 | 10456 | 84 | 62 | 73.8095 | |
| qzeng-custom | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.3281 | 98.8960 | 97.7666 | 73.6710 | 9585 | 107 | 9718 | 222 | 62 | 27.9279 | |
| qzeng-custom | SNP | tv | map_l100_m2_e1 | homalt | 87.7555 | 78.7143 | 99.1432 | 62.9833 | 7322 | 1980 | 7290 | 63 | 62 | 98.4127 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.4121 | 97.3169 | 99.5323 | 46.2505 | 21653 | 597 | 21709 | 102 | 62 | 60.7843 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 87.8594 | 97.1731 | 80.1749 | 65.9384 | 275 | 8 | 275 | 68 | 62 | 91.1765 | |
| eyeh-varpipe | INDEL | * | map_l125_m1_e0 | * | 96.4644 | 96.0133 | 96.9198 | 94.1307 | 2023 | 84 | 2769 | 88 | 62 | 70.4545 | |
| dgrover-gatk | SNP | * | map_l100_m1_e0 | het | 99.3755 | 99.4665 | 99.2846 | 70.4056 | 45117 | 242 | 45106 | 325 | 62 | 19.0769 | |
| 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 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 82.8342 | 75.6494 | 91.5271 | 45.0163 | 932 | 300 | 929 | 86 | 62 | 72.0930 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3863 | 99.8976 | 96.9200 | 41.5335 | 1951 | 2 | 1951 | 62 | 62 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3615 | 99.8976 | 96.8719 | 41.6063 | 1951 | 2 | 1951 | 63 | 62 | 98.4127 | |
| ckim-vqsr | SNP | ti | * | het | 99.5238 | 99.1280 | 99.9229 | 24.8520 | 1270713 | 11178 | 1270665 | 981 | 62 | 6.3201 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 85.3274 | 76.4173 | 96.5895 | 46.1939 | 2278 | 703 | 2294 | 81 | 62 | 76.5432 | |