PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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72601-72650 / 86044 show all | |||||||||||||||
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 8.5511 | 4.6512 | 52.9412 | 66.0000 | 8 | 164 | 9 | 8 | 3 | 37.5000 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 18.4985 | 11.8280 | 42.4242 | 51.4706 | 22 | 164 | 70 | 95 | 84 | 88.4211 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 85.6750 | 96.3113 | 77.1544 | 58.1338 | 4282 | 164 | 4978 | 1474 | 1427 | 96.8114 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 91.3456 | 85.6266 | 97.8831 | 68.3472 | 977 | 164 | 971 | 21 | 20 | 95.2381 | |
| hfeng-pmm2 | INDEL | I16_PLUS | HG002compoundhet | * | 94.8024 | 92.3472 | 97.3917 | 52.6892 | 1979 | 164 | 1979 | 53 | 52 | 98.1132 | |
| dgrover-gatk | SNP | * | map_l150_m1_e0 | het | 98.9459 | 99.1510 | 98.7416 | 80.1493 | 19152 | 164 | 19146 | 244 | 49 | 20.0820 | |
| dgrover-gatk | SNP | ti | map_l100_m0_e0 | * | 99.2854 | 99.2467 | 99.3242 | 70.6721 | 21607 | 164 | 21604 | 147 | 34 | 23.1293 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.5105 | 95.6899 | 99.4017 | 30.5702 | 3641 | 164 | 3655 | 22 | 22 | 100.0000 | |
| egarrison-hhga | SNP | ti | map_l125_m0_e0 | * | 99.2437 | 98.7149 | 99.7782 | 73.5653 | 12598 | 164 | 12598 | 28 | 14 | 50.0000 | |
| ckim-vqsr | SNP | tv | segdup | * | 98.8248 | 98.0778 | 99.5833 | 94.7773 | 8368 | 164 | 8364 | 35 | 5 | 14.2857 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 89.4737 | 82.0175 | 98.4211 | 51.7154 | 748 | 164 | 748 | 12 | 4 | 33.3333 | |
| ckim-isaac | INDEL | D1_5 | map_l100_m0_e0 | het | 83.0777 | 72.2504 | 97.7221 | 87.1675 | 427 | 164 | 429 | 10 | 3 | 30.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 82.1817 | 76.4706 | 88.8147 | 52.8718 | 533 | 164 | 532 | 67 | 66 | 98.5075 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 82.1817 | 76.4706 | 88.8147 | 52.8718 | 533 | 164 | 532 | 67 | 66 | 98.5075 | |
| ckim-dragen | SNP | * | map_l100_m2_e1 | homalt | 99.6376 | 99.4100 | 99.8663 | 58.3837 | 27632 | 164 | 27637 | 37 | 33 | 89.1892 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.6346 | 95.8110 | 93.4868 | 75.2785 | 3751 | 164 | 3818 | 266 | 220 | 82.7068 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 5.7143 | 0.0000 | 0.0000 | 10 | 165 | 0 | 0 | 0 | ||
| asubramanian-gatk | SNP | tv | HG002compoundhet | het | 98.0320 | 96.4691 | 99.6463 | 55.8548 | 4508 | 165 | 4508 | 16 | 9 | 56.2500 | |
| bgallagher-sentieon | INDEL | D1_5 | HG002complexvar | * | 99.6177 | 99.4956 | 99.7400 | 58.4446 | 32550 | 165 | 32605 | 85 | 76 | 89.4118 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.3977 | 98.8829 | 99.9179 | 55.5579 | 14605 | 165 | 14609 | 12 | 3 | 25.0000 | |
| ndellapenna-hhga | SNP | ti | map_l150_m0_e0 | het | 98.1786 | 96.7628 | 99.6364 | 79.7339 | 4932 | 165 | 4932 | 18 | 7 | 38.8889 | |
| jmaeng-gatk | SNP | * | HG002compoundhet | het | 99.2949 | 98.8362 | 99.7579 | 46.8998 | 14013 | 165 | 14011 | 34 | 28 | 82.3529 | |
| raldana-dualsentieon | INDEL | I1_5 | HG002complexvar | hetalt | 94.9524 | 90.4403 | 99.9382 | 69.6987 | 1561 | 165 | 1618 | 1 | 1 | 100.0000 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.0139 | 98.4069 | 99.6285 | 44.6543 | 10192 | 165 | 10191 | 38 | 37 | 97.3684 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 19.3103 | 11.2903 | 66.6667 | 90.9366 | 21 | 165 | 20 | 10 | 9 | 90.0000 | |
| ghariani-varprowl | SNP | * | HG002complexvar | homalt | 99.6051 | 99.9428 | 99.2696 | 21.6199 | 288407 | 165 | 288526 | 2123 | 1441 | 67.8756 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 61.8951 | 85.0543 | 48.6486 | 86.3559 | 939 | 165 | 900 | 950 | 47 | 4.9474 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 19.8656 | 11.2903 | 82.6087 | 87.7660 | 21 | 165 | 19 | 4 | 3 | 75.0000 | |
| gduggal-bwafb | INDEL | D6_15 | HG002complexvar | hetalt | 88.4177 | 83.7117 | 93.6842 | 66.0714 | 848 | 165 | 178 | 12 | 12 | 100.0000 | |
| gduggal-bwafb | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.7961 | 98.2976 | 95.3398 | 72.9184 | 9527 | 165 | 9554 | 467 | 126 | 26.9807 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 89.1443 | 80.8806 | 99.2888 | 68.7833 | 698 | 165 | 698 | 5 | 4 | 80.0000 | |
| gduggal-bwaplat | INDEL | I1_5 | map_l125_m1_e0 | het | 79.2593 | 66.0494 | 99.0741 | 94.2776 | 321 | 165 | 321 | 3 | 1 | 33.3333 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 0.0000 | 87.2192 | 0.0000 | 0.0000 | 1126 | 165 | 0 | 0 | 0 | ||
| ciseli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 53.2420 | 85.0543 | 38.7490 | 79.7595 | 939 | 165 | 985 | 1557 | 105 | 6.7437 | |
| ciseli-custom | SNP | tv | segdup | * | 95.0488 | 98.0661 | 92.2117 | 92.0351 | 8367 | 165 | 8347 | 705 | 88 | 12.4823 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 80.5755 | 83.5821 | 77.7778 | 62.2922 | 840 | 165 | 847 | 242 | 95 | 39.2562 | |
| ciseli-custom | INDEL | I1_5 | map_l125_m2_e0 | het | 64.4414 | 66.8008 | 62.2430 | 89.2549 | 332 | 165 | 333 | 202 | 174 | 86.1386 | |
| ckim-gatk | INDEL | I16_PLUS | HG002compoundhet | hetalt | 95.8494 | 92.1166 | 99.8975 | 44.7808 | 1928 | 165 | 1950 | 2 | 2 | 100.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.9210 | 92.2462 | 93.6058 | 72.7642 | 1963 | 165 | 1947 | 133 | 117 | 87.9699 | |
| jlack-gatk | SNP | * | map_l250_m2_e0 | * | 93.5078 | 97.9074 | 89.4865 | 92.8768 | 7720 | 165 | 7720 | 907 | 67 | 7.3870 | |
| dgrover-gatk | SNP | * | map_l150_m2_e0 | het | 98.9689 | 99.1805 | 98.7582 | 81.1353 | 19968 | 165 | 19962 | 251 | 50 | 19.9203 | |
| dgrover-gatk | SNP | * | map_l150_m2_e1 | het | 98.9757 | 99.1897 | 98.7625 | 81.1801 | 20198 | 165 | 20192 | 253 | 50 | 19.7628 | |
| dgrover-gatk | SNP | tv | map_siren | * | 99.6255 | 99.6408 | 99.6103 | 59.7727 | 45765 | 165 | 45757 | 179 | 35 | 19.5531 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 96.8750 | 93.9737 | 99.9612 | 23.5381 | 2573 | 165 | 2575 | 1 | 0 | 0.0000 | |
| dgrover-gatk | SNP | ti | map_l150_m2_e0 | * | 99.2366 | 99.1907 | 99.2825 | 78.2548 | 20346 | 166 | 20342 | 147 | 36 | 24.4898 | |
| dgrover-gatk | SNP | ti | map_l150_m2_e1 | * | 99.2396 | 99.1990 | 99.2803 | 78.3146 | 20557 | 166 | 20553 | 149 | 36 | 24.1611 | |
| egarrison-hhga | INDEL | * | map_siren | * | 97.8660 | 97.7598 | 97.9724 | 96.4159 | 7244 | 166 | 7248 | 150 | 78 | 52.0000 | |
| gduggal-snapvard | SNP | * | map_l250_m2_e0 | homalt | 96.5678 | 93.8198 | 99.4817 | 88.0057 | 2520 | 166 | 2495 | 13 | 9 | 69.2308 | |
| gduggal-snapplat | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 72.2480 | 83.2661 | 63.8051 | 90.8950 | 826 | 166 | 825 | 468 | 9 | 1.9231 | |
| gduggal-snapvard | INDEL | * | map_siren | hetalt | 0.0000 | 32.7935 | 0.0000 | 0.0000 | 81 | 166 | 0 | 0 | 0 | ||