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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
55451-55500 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.8506 | 100.0000 | 97.7273 | 77.8894 | 43 | 0 | 43 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.1228 | 96.5257 | 97.7273 | 78.8316 | 639 | 23 | 602 | 14 | 8 | 57.1429 | |
| ltrigg-rtg1 | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 97.7273 | 96.1027 | 0 | 0 | 43 | 1 | 1 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I1_5 | map_l100_m2_e1 | hetalt | 93.0988 | 88.8889 | 97.7273 | 93.3333 | 40 | 5 | 43 | 1 | 1 | 100.0000 | |
| jli-custom | SNP | * | map_l100_m2_e1 | hetalt | 98.8506 | 100.0000 | 97.7273 | 74.8571 | 43 | 0 | 43 | 1 | 1 | 100.0000 | |
| jli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.5057 | 97.2851 | 97.7273 | 90.8676 | 215 | 6 | 215 | 5 | 2 | 40.0000 | |
| jli-custom | SNP | tv | map_l100_m2_e1 | hetalt | 98.8506 | 100.0000 | 97.7273 | 74.8571 | 43 | 0 | 43 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 92.1830 | 87.2340 | 97.7273 | 64.2276 | 41 | 6 | 43 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.8506 | 100.0000 | 97.7273 | 77.0833 | 43 | 0 | 43 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.9996 | 94.3320 | 97.7273 | 81.2766 | 233 | 14 | 215 | 5 | 3 | 60.0000 | |
| ltrigg-rtg1 | INDEL | I6_15 | map_siren | het | 95.3087 | 93.0070 | 97.7273 | 76.9231 | 133 | 10 | 129 | 3 | 1 | 33.3333 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.8506 | 100.0000 | 97.7273 | 77.5510 | 43 | 0 | 43 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.1978 | 94.7154 | 97.7273 | 88.4393 | 233 | 13 | 215 | 5 | 3 | 60.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l100_m1_e0 | hetalt | 94.5055 | 91.4894 | 97.7273 | 89.3462 | 43 | 4 | 43 | 1 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.8506 | 100.0000 | 97.7273 | 77.7778 | 43 | 0 | 43 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 90.8989 | 84.9624 | 97.7273 | 86.2069 | 113 | 20 | 129 | 3 | 3 | 100.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 93.0561 | 88.8112 | 97.7273 | 51.9782 | 254 | 32 | 344 | 8 | 8 | 100.0000 | |
| asubramanian-gatk | INDEL | I1_5 | map_l100_m2_e1 | hetalt | 96.6292 | 95.5556 | 97.7273 | 90.1345 | 43 | 2 | 43 | 1 | 0 | 0.0000 | |
| ndellapenna-hhga | INDEL | I6_15 | map_siren | homalt | 96.6292 | 95.5556 | 97.7273 | 81.5514 | 86 | 4 | 86 | 2 | 2 | 100.0000 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.8506 | 100.0000 | 97.7273 | 76.5957 | 43 | 0 | 43 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | I1_5 | map_l250_m2_e0 | homalt | 96.6292 | 95.5556 | 97.7273 | 94.5342 | 43 | 2 | 43 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | INDEL | D1_5 | map_siren | hetalt | 84.8684 | 75.0000 | 97.7273 | 92.9487 | 63 | 21 | 43 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | INDEL | D16_PLUS | map_l100_m2_e1 | * | 60.9929 | 44.3299 | 97.7273 | 95.8015 | 43 | 54 | 43 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 68.2540 | 52.4390 | 97.7273 | 85.7605 | 43 | 39 | 43 | 1 | 1 | 100.0000 | |
| jli-custom | INDEL | D1_5 | map_l100_m2_e1 | hetalt | 89.3838 | 82.3529 | 97.7273 | 91.6667 | 42 | 9 | 43 | 1 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.8506 | 100.0000 | 97.7273 | 76.7196 | 43 | 0 | 43 | 1 | 1 | 100.0000 | |
| jpowers-varprowl | SNP | tv | map_l100_m1_e0 | * | 97.6764 | 97.6246 | 97.7283 | 72.0238 | 23919 | 582 | 23919 | 556 | 138 | 24.8201 | |
| eyeh-varpipe | INDEL | D1_5 | map_l125_m2_e1 | * | 97.8272 | 97.9257 | 97.7289 | 86.7675 | 1133 | 24 | 1377 | 32 | 17 | 53.1250 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 94.8647 | 92.1636 | 97.7290 | 70.8955 | 26462 | 2250 | 26465 | 615 | 21 | 3.4146 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 94.8647 | 92.1636 | 97.7290 | 70.8955 | 26462 | 2250 | 26465 | 615 | 21 | 3.4146 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l100_m2_e0 | het | 98.4217 | 99.1242 | 97.7291 | 84.1426 | 1245 | 11 | 1248 | 29 | 2 | 6.8966 | |
| egarrison-hhga | INDEL | D1_5 | map_l100_m2_e1 | het | 98.0355 | 98.3438 | 97.7291 | 83.2875 | 1247 | 21 | 1248 | 29 | 8 | 27.5862 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 96.1245 | 94.5714 | 97.7295 | 52.4859 | 993 | 57 | 990 | 23 | 9 | 39.1304 | |
| ckim-vqsr | INDEL | * | map_l100_m2_e0 | * | 97.1833 | 96.6423 | 97.7304 | 89.4395 | 3569 | 124 | 3574 | 83 | 16 | 19.2771 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.3971 | 97.0646 | 97.7319 | 53.7356 | 14351 | 434 | 14349 | 333 | 323 | 96.9970 | |
| raldana-dualsentieon | INDEL | I1_5 | map_l125_m1_e0 | het | 97.4247 | 97.1193 | 97.7320 | 84.0145 | 472 | 14 | 474 | 11 | 0 | 0.0000 | |
| ghariani-varprowl | SNP | ti | map_l125_m2_e1 | * | 98.2162 | 98.7046 | 97.7326 | 76.3818 | 30173 | 396 | 30173 | 700 | 158 | 22.5714 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 95.0368 | 92.4855 | 97.7328 | 30.1370 | 1600 | 130 | 1595 | 37 | 31 | 83.7838 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.4319 | 93.2367 | 97.7330 | 74.4530 | 386 | 28 | 388 | 9 | 9 | 100.0000 | |
| hfeng-pmm2 | SNP | tv | map_l250_m2_e0 | het | 97.7583 | 97.7835 | 97.7331 | 90.3173 | 1897 | 43 | 1897 | 44 | 3 | 6.8182 | |
| ckim-dragen | SNP | * | map_l125_m2_e0 | * | 98.4092 | 99.0947 | 97.7332 | 74.8209 | 46300 | 423 | 46306 | 1074 | 120 | 11.1732 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 50.3229 | 33.8852 | 97.7333 | 47.5634 | 1617 | 3155 | 2587 | 60 | 56 | 93.3333 | |
| egarrison-hhga | INDEL | D1_5 | segdup | * | 97.7335 | 97.7335 | 97.7335 | 94.3200 | 1078 | 25 | 1078 | 25 | 22 | 88.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | HG002compoundhet | * | 95.0875 | 92.5805 | 97.7340 | 52.1790 | 1984 | 159 | 1984 | 46 | 45 | 97.8261 | |
| ltrigg-rtg2 | SNP | tv | segdup | het | 98.5667 | 99.4137 | 97.7340 | 87.6779 | 5256 | 31 | 5262 | 122 | 2 | 1.6393 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.8473 | 94.0320 | 97.7341 | 82.3702 | 646 | 41 | 647 | 15 | 12 | 80.0000 | |
| eyeh-varpipe | SNP | * | map_siren | * | 98.7590 | 99.8051 | 97.7347 | 59.1101 | 145943 | 285 | 141168 | 3272 | 81 | 2.4756 | |
| gduggal-bwaplat | SNP | tv | HG002compoundhet | homalt | 94.3411 | 91.1747 | 97.7352 | 50.1035 | 3089 | 299 | 3064 | 71 | 67 | 94.3662 | |
| rpoplin-dv42 | INDEL | D6_15 | HG002complexvar | het | 97.7459 | 97.7564 | 97.7354 | 59.1947 | 3050 | 70 | 3021 | 70 | 62 | 88.5714 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.8519 | 95.9843 | 97.7354 | 64.7626 | 3418 | 143 | 3539 | 82 | 70 | 85.3659 | |