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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
11101-11150 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 95.3412 | 95.1435 | 95.5397 | 38.5245 | 3879 | 198 | 3877 | 181 | 170 | 93.9227 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 53.7560 | 79.3033 | 40.6582 | 61.4881 | 387 | 101 | 383 | 559 | 525 | 93.9177 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.6756 | 98.7256 | 98.6257 | 64.1796 | 8289 | 107 | 8253 | 115 | 108 | 93.9130 | |
| anovak-vg | INDEL | * | map_siren | homalt | 77.1234 | 89.6798 | 67.6512 | 75.5300 | 2381 | 274 | 2405 | 1150 | 1080 | 93.9130 | |
| anovak-vg | INDEL | I1_5 | map_l100_m1_e0 | homalt | 67.3385 | 92.8571 | 52.8222 | 77.1699 | 481 | 37 | 496 | 443 | 416 | 93.9052 | |
| gduggal-bwaplat | SNP | tv | HG002complexvar | homalt | 97.7875 | 95.7534 | 99.9100 | 24.5806 | 91072 | 4039 | 90999 | 82 | 77 | 93.9024 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 70.5915 | 71.0059 | 70.1818 | 64.6075 | 120 | 49 | 193 | 82 | 77 | 93.9024 | |
| hfeng-pmm1 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.9642 | 97.6007 | 96.3360 | 64.2948 | 2156 | 53 | 2156 | 82 | 77 | 93.9024 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.0590 | 97.3516 | 98.7767 | 53.3290 | 17203 | 468 | 17199 | 213 | 200 | 93.8967 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.0590 | 97.3516 | 98.7767 | 53.3290 | 17203 | 468 | 17199 | 213 | 200 | 93.8967 | |
| jli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.9784 | 98.5004 | 99.4611 | 39.0941 | 24172 | 368 | 24179 | 131 | 123 | 93.8931 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 93.3528 | 88.7263 | 98.4883 | 45.1727 | 8248 | 1048 | 8535 | 131 | 123 | 93.8931 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.9978 | 94.1236 | 97.9483 | 47.9502 | 6503 | 406 | 8593 | 180 | 169 | 93.8889 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.7777 | 99.3930 | 98.1700 | 65.9733 | 12445 | 76 | 12285 | 229 | 215 | 93.8865 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 80.6298 | 89.3985 | 73.4276 | 74.6915 | 1189 | 141 | 1039 | 376 | 353 | 93.8830 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 79.4110 | 79.6748 | 79.1489 | 83.7595 | 196 | 50 | 186 | 49 | 46 | 93.8776 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 65.8913 | 84.0000 | 54.2056 | 64.5695 | 42 | 8 | 58 | 49 | 46 | 93.8776 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 90.1124 | 96.0968 | 84.8297 | 79.1299 | 1748 | 71 | 1644 | 294 | 276 | 93.8776 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 90.1124 | 96.0968 | 84.8297 | 79.1299 | 1748 | 71 | 1644 | 294 | 276 | 93.8776 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 92.5543 | 91.9137 | 93.2039 | 71.7808 | 682 | 60 | 672 | 49 | 46 | 93.8776 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 82.8070 | 95.5800 | 0 | 0 | 236 | 49 | 46 | 93.8776 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 75.4767 | 66.4516 | 87.3385 | 73.7805 | 103 | 52 | 338 | 49 | 46 | 93.8776 | |
| hfeng-pmm1 | INDEL | * | HG002compoundhet | het | 86.5457 | 82.4866 | 91.0249 | 77.7276 | 3377 | 717 | 3144 | 310 | 291 | 93.8710 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 91.1226 | 86.4620 | 96.3144 | 38.7578 | 4956 | 776 | 18319 | 701 | 658 | 93.8659 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.6262 | 97.1247 | 98.1330 | 61.8291 | 42089 | 1246 | 41891 | 797 | 748 | 93.8519 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 94.9234 | 99.0868 | 91.0959 | 82.4814 | 868 | 8 | 665 | 65 | 61 | 93.8462 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 65.9384 | 80.0000 | 56.0811 | 49.8305 | 108 | 27 | 83 | 65 | 61 | 93.8462 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | * | 50.5051 | 47.7707 | 53.5714 | 69.8925 | 75 | 82 | 75 | 65 | 61 | 93.8462 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 76.1553 | 85.1190 | 68.8995 | 75.1486 | 143 | 25 | 144 | 65 | 61 | 93.8462 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.6606 | 99.5951 | 97.7434 | 43.6301 | 5658 | 23 | 5631 | 130 | 122 | 93.8462 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.7214 | 99.2652 | 98.1834 | 66.0056 | 12429 | 92 | 12269 | 227 | 213 | 93.8326 | |
| anovak-vg | INDEL | I1_5 | map_l100_m0_e0 | homalt | 67.9183 | 93.2692 | 53.4031 | 79.4954 | 194 | 14 | 204 | 178 | 167 | 93.8202 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.9553 | 99.4146 | 96.5382 | 63.5394 | 2717 | 16 | 2705 | 97 | 91 | 93.8144 | |
| ndellapenna-hhga | SNP | * | HG002compoundhet | homalt | 98.7381 | 99.4064 | 98.0787 | 35.7852 | 10718 | 64 | 10720 | 210 | 197 | 93.8095 | |
| anovak-vg | INDEL | I1_5 | map_l100_m2_e0 | homalt | 67.4017 | 92.6554 | 52.9657 | 79.0814 | 492 | 39 | 509 | 452 | 424 | 93.8053 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.4366 | 98.2863 | 98.5874 | 60.3465 | 15772 | 275 | 15773 | 226 | 212 | 93.8053 | |
| mlin-fermikit | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.8486 | 98.4572 | 99.2431 | 55.7060 | 16912 | 265 | 16914 | 129 | 121 | 93.7984 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 61.4597 | 44.8804 | 97.4636 | 72.8689 | 2665 | 3273 | 4957 | 129 | 121 | 93.7984 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 88.8814 | 87.5486 | 90.2554 | 74.8436 | 1350 | 192 | 1343 | 145 | 136 | 93.7931 | |
| gduggal-snapvard | INDEL | * | * | homalt | 86.7363 | 77.5779 | 98.3465 | 41.7135 | 97105 | 28066 | 99624 | 1675 | 1571 | 93.7910 | |
| mlin-fermikit | SNP | * | map_l150_m2_e1 | homalt | 61.0704 | 52.1941 | 73.5845 | 61.1854 | 6173 | 5654 | 6173 | 2216 | 2078 | 93.7726 | |
| ckim-vqsr | INDEL | I6_15 | * | * | 97.6524 | 96.7691 | 98.5520 | 52.9508 | 24021 | 802 | 24026 | 353 | 331 | 93.7677 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.1938 | 98.9533 | 97.4458 | 67.6938 | 14464 | 153 | 14078 | 369 | 346 | 93.7669 | |
| ciseli-custom | INDEL | I1_5 | HG002compoundhet | * | 12.1122 | 9.5913 | 16.4310 | 70.5188 | 1185 | 11170 | 1255 | 6383 | 5985 | 93.7647 | |
| cchapple-custom | INDEL | * | HG002compoundhet | * | 95.5576 | 93.9686 | 97.2012 | 57.1714 | 28153 | 1807 | 51191 | 1474 | 1382 | 93.7585 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 94.3593 | 92.2917 | 96.5217 | 82.2462 | 443 | 37 | 444 | 16 | 15 | 93.7500 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.6664 | 95.9541 | 99.4410 | 50.6296 | 5692 | 240 | 5692 | 32 | 30 | 93.7500 | |
| anovak-vg | SNP | ti | func_cds | homalt | 99.1630 | 98.9384 | 99.3887 | 18.9378 | 5219 | 56 | 5203 | 32 | 30 | 93.7500 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 35.4839 | 31.4286 | 40.7407 | 83.1250 | 11 | 24 | 11 | 16 | 15 | 93.7500 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.5290 | 95.6844 | 99.4462 | 41.4708 | 5676 | 256 | 5746 | 32 | 30 | 93.7500 | |