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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
35251-35300 / 86044 show all | |||||||||||||||
| gduggal-snapplat | INDEL | * | HG002complexvar | hetalt | 48.8074 | 34.6851 | 82.3281 | 84.4012 | 1283 | 2416 | 1365 | 293 | 225 | 76.7918 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 51.5152 | 34.6939 | 100.0000 | 32.0000 | 17 | 32 | 17 | 0 | 0 | ||
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 0.0000 | 34.7305 | 0.0000 | 0.0000 | 58 | 109 | 0 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 51.2669 | 34.7444 | 97.7528 | 56.7121 | 435 | 817 | 435 | 10 | 10 | 100.0000 | |
| asubramanian-gatk | SNP | ti | map_l125_m2_e0 | het | 51.5556 | 34.7637 | 99.7264 | 92.2284 | 6562 | 12314 | 6560 | 18 | 6 | 33.3333 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 42.2807 | 34.7724 | 53.9244 | 82.6368 | 1780 | 3339 | 2068 | 1767 | 59 | 3.3390 | |
| gduggal-snapplat | INDEL | D6_15 | map_l150_m2_e0 | het | 45.7143 | 34.7826 | 66.6667 | 96.1340 | 16 | 30 | 10 | 5 | 1 | 20.0000 | |
| anovak-vg | INDEL | * | map_l150_m2_e1 | hetalt | 0.0000 | 34.7826 | 0.0000 | 0.0000 | 8 | 15 | 0 | 0 | 0 | ||
| mlin-fermikit | INDEL | D1_5 | map_l250_m0_e0 | * | 46.3768 | 34.7826 | 69.5652 | 93.9153 | 16 | 30 | 16 | 7 | 6 | 85.7143 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 0.0000 | 34.8485 | 0.0000 | 0.0000 | 46 | 86 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | * | map_l125_m2_e1 | hetalt | 0.0000 | 34.8837 | 0.0000 | 0.0000 | 15 | 28 | 0 | 0 | 0 | ||
| asubramanian-gatk | SNP | * | map_l100_m2_e1 | hetalt | 51.7241 | 34.8837 | 100.0000 | 90.7407 | 15 | 28 | 15 | 0 | 0 | ||
| asubramanian-gatk | SNP | tv | map_l100_m2_e1 | hetalt | 51.7241 | 34.8837 | 100.0000 | 90.6832 | 15 | 28 | 15 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 51.2821 | 34.8837 | 96.7742 | 79.1946 | 30 | 56 | 30 | 1 | 1 | 100.0000 | |
| ckim-vqsr | SNP | * | map_l100_m2_e1 | hetalt | 51.7241 | 34.8837 | 100.0000 | 94.6237 | 15 | 28 | 15 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | map_l100_m2_e1 | hetalt | 51.7241 | 34.8837 | 100.0000 | 94.6237 | 15 | 28 | 15 | 0 | 0 | ||
| gduggal-snapplat | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 23.7011 | 34.8943 | 17.9449 | 88.9091 | 231 | 431 | 241 | 1102 | 10 | 0.9074 | |
| mlin-fermikit | INDEL | I1_5 | map_l125_m0_e0 | het | 51.5385 | 34.8958 | 98.5294 | 81.9629 | 67 | 125 | 67 | 1 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 46.1240 | 34.8974 | 68.0000 | 71.9101 | 119 | 222 | 17 | 8 | 8 | 100.0000 | |
| gduggal-snapplat | INDEL | * | HG002compoundhet | het | 24.1644 | 34.9047 | 18.4785 | 71.1703 | 1429 | 2665 | 1727 | 7619 | 2083 | 27.3395 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 51.1480 | 34.9051 | 95.6654 | 53.7872 | 2813 | 5246 | 2825 | 128 | 108 | 84.3750 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 51.1480 | 34.9051 | 95.6654 | 53.7872 | 2813 | 5246 | 2825 | 128 | 108 | 84.3750 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 50.1080 | 34.9234 | 88.6547 | 58.7648 | 1984 | 3697 | 1977 | 253 | 213 | 84.1897 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 50.1828 | 34.9234 | 89.1245 | 58.3302 | 1984 | 3697 | 1975 | 241 | 212 | 87.9668 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 47.0793 | 34.9282 | 72.1951 | 63.7809 | 146 | 272 | 148 | 57 | 56 | 98.2456 | |
| anovak-vg | INDEL | I6_15 | map_siren | het | 45.1108 | 34.9650 | 63.5514 | 79.0607 | 50 | 93 | 68 | 39 | 11 | 28.2051 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 51.0807 | 34.9679 | 94.7321 | 49.3900 | 1091 | 2029 | 1061 | 59 | 45 | 76.2712 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 46.4146 | 34.9744 | 68.9769 | 73.6604 | 2941 | 5468 | 2926 | 1316 | 1208 | 91.7933 | |
| asubramanian-gatk | SNP | ti | map_l125_m2_e1 | het | 51.8016 | 34.9872 | 99.7311 | 92.1950 | 6678 | 12409 | 6676 | 18 | 6 | 33.3333 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 50.4626 | 34.9887 | 90.4762 | 43.6782 | 155 | 288 | 133 | 14 | 11 | 78.5714 | |
| gduggal-snapplat | INDEL | D6_15 | map_l150_m0_e0 | het | 48.6957 | 35.0000 | 80.0000 | 97.7578 | 7 | 13 | 4 | 1 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 47.7273 | 35.0000 | 75.0000 | 70.9091 | 133 | 247 | 24 | 8 | 8 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | map_l100_m0_e0 | het | 51.2195 | 35.0000 | 95.4545 | 93.0380 | 21 | 39 | 21 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 44.8723 | 35.0206 | 62.4365 | 72.5902 | 2214 | 4108 | 2214 | 1332 | 1288 | 96.6967 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 44.8723 | 35.0206 | 62.4365 | 72.5902 | 2214 | 4108 | 2214 | 1332 | 1288 | 96.6967 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 49.7009 | 35.0282 | 85.5263 | 70.6564 | 62 | 115 | 65 | 11 | 10 | 90.9091 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 0.0000 | 35.0515 | 0.0000 | 0.0000 | 34 | 63 | 0 | 0 | 0 | ||
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 49.6249 | 35.0531 | 84.9315 | 68.9362 | 231 | 428 | 62 | 11 | 11 | 100.0000 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 49.6249 | 35.0531 | 84.9315 | 68.9362 | 231 | 428 | 62 | 11 | 11 | 100.0000 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 4.4684 | 35.0877 | 2.3861 | 92.1778 | 20 | 37 | 22 | 900 | 12 | 1.3333 | |
| ckim-isaac | INDEL | D1_5 | map_l250_m1_e0 | homalt | 51.9481 | 35.0877 | 100.0000 | 93.7695 | 20 | 37 | 20 | 0 | 0 | ||
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 42.3077 | 35.1064 | 53.2258 | 74.8988 | 66 | 122 | 66 | 58 | 49 | 84.4828 | |
| gduggal-snapplat | INDEL | D6_15 | map_l125_m2_e1 | homalt | 52.0000 | 35.1351 | 100.0000 | 94.7712 | 13 | 24 | 8 | 0 | 0 | ||
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 50.7551 | 35.1351 | 91.3793 | 30.4000 | 52 | 96 | 318 | 30 | 28 | 93.3333 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 0.0000 | 35.1351 | 0.0000 | 0.0000 | 26 | 48 | 0 | 0 | 0 | ||
| gduggal-snapplat | INDEL | D6_15 | * | hetalt | 51.3567 | 35.1358 | 95.3989 | 60.4943 | 2872 | 5302 | 2882 | 139 | 111 | 79.8561 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 30.6069 | 35.1515 | 27.1028 | 96.8469 | 58 | 107 | 58 | 156 | 7 | 4.4872 | |
| gduggal-bwaplat | SNP | * | map_l250_m1_e0 | * | 51.9747 | 35.1703 | 99.5300 | 97.3642 | 2540 | 4682 | 2541 | 12 | 3 | 25.0000 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 51.3821 | 35.1740 | 95.2929 | 41.6005 | 930 | 1714 | 911 | 45 | 35 | 77.7778 | |
| gduggal-snapplat | INDEL | D6_15 | HG002compoundhet | hetalt | 51.7417 | 35.1859 | 97.7226 | 44.3646 | 2868 | 5283 | 2875 | 67 | 52 | 77.6119 | |