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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
12901-12950 / 86044 show all | |||||||||||||||
| gduggal-snapfb | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 79.8568 | 84.6127 | 75.6070 | 64.0420 | 4850 | 882 | 3394 | 1095 | 247 | 22.5571 | |
| raldana-dualsentieon | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 91.8485 | 84.9895 | 99.9117 | 39.0086 | 3250 | 574 | 3393 | 3 | 3 | 100.0000 | |
| ckim-vqsr | SNP | ti | map_l125_m1_e0 | homalt | 46.9945 | 30.7198 | 99.9411 | 85.1863 | 3393 | 7652 | 3393 | 2 | 2 | 100.0000 | |
| gduggal-snapfb | INDEL | * | map_l100_m2_e0 | * | 93.4957 | 91.3079 | 95.7910 | 84.8783 | 3372 | 321 | 3391 | 149 | 39 | 26.1745 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.3835 | 94.9801 | 99.9116 | 43.2609 | 3349 | 177 | 3390 | 3 | 3 | 100.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.3835 | 94.9801 | 99.9116 | 43.2609 | 3349 | 177 | 3390 | 3 | 3 | 100.0000 | |
| anovak-vg | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 97.2061 | 97.3623 | 97.0504 | 40.0412 | 3359 | 91 | 3389 | 103 | 49 | 47.5728 | |
| ghariani-varprowl | SNP | tv | HG002compoundhet | homalt | 83.7163 | 99.8524 | 72.0698 | 50.4793 | 3383 | 5 | 3388 | 1313 | 1124 | 85.6055 | |
| jpowers-varprowl | SNP | tv | HG002compoundhet | homalt | 83.3558 | 99.8524 | 71.5372 | 51.1753 | 3383 | 5 | 3388 | 1348 | 1126 | 83.5312 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 76.6225 | 63.6808 | 96.1659 | 75.3638 | 3384 | 1930 | 3386 | 135 | 45 | 33.3333 | |
| gduggal-bwafb | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.6157 | 97.9161 | 99.3253 | 64.1874 | 3383 | 72 | 3386 | 23 | 21 | 91.3043 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.3256 | 94.9234 | 99.8525 | 39.2800 | 3347 | 179 | 3385 | 5 | 5 | 100.0000 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.3256 | 94.9234 | 99.8525 | 39.2800 | 3347 | 179 | 3385 | 5 | 5 | 100.0000 | |
| ciseli-custom | SNP | ti | map_l150_m0_e0 | het | 72.0997 | 66.3920 | 78.8811 | 87.9805 | 3384 | 1713 | 3384 | 906 | 29 | 3.2009 | |
| ciseli-custom | SNP | tv | map_l150_m2_e0 | homalt | 85.5692 | 82.9537 | 88.3551 | 74.3676 | 3387 | 696 | 3384 | 446 | 347 | 77.8027 | |
| ckim-dragen | SNP | tv | HG002compoundhet | homalt | 99.8672 | 99.8819 | 99.8524 | 43.2020 | 3384 | 4 | 3383 | 5 | 5 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.1878 | 96.9931 | 99.4123 | 51.7989 | 3387 | 105 | 3383 | 20 | 14 | 70.0000 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6386 | 95.9000 | 99.4413 | 58.6605 | 3415 | 146 | 3382 | 19 | 14 | 73.6842 | |
| hfeng-pmm3 | SNP | tv | HG002compoundhet | homalt | 99.8376 | 99.8229 | 99.8524 | 42.5250 | 3382 | 6 | 3382 | 5 | 5 | 100.0000 | |
| hfeng-pmm1 | SNP | tv | HG002compoundhet | homalt | 99.8229 | 99.7934 | 99.8523 | 42.7460 | 3381 | 7 | 3381 | 5 | 5 | 100.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.2350 | 94.7249 | 99.8818 | 43.0518 | 3340 | 186 | 3381 | 4 | 4 | 100.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.2350 | 94.7249 | 99.8818 | 43.0518 | 3340 | 186 | 3381 | 4 | 4 | 100.0000 | |
| bgallagher-sentieon | SNP | tv | HG002compoundhet | homalt | 99.8524 | 99.9115 | 99.7933 | 42.7775 | 3385 | 3 | 3380 | 7 | 6 | 85.7143 | |
| hfeng-pmm2 | SNP | tv | HG002compoundhet | homalt | 99.7933 | 99.7639 | 99.8228 | 43.5008 | 3380 | 8 | 3380 | 6 | 5 | 83.3333 | |
| jli-custom | SNP | tv | HG002compoundhet | homalt | 99.8081 | 99.7934 | 99.8228 | 43.2831 | 3381 | 7 | 3380 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | tv | HG002compoundhet | homalt | 99.8671 | 99.9115 | 99.8228 | 42.6879 | 3385 | 3 | 3380 | 6 | 5 | 83.3333 | |
| raldana-dualsentieon | SNP | tv | HG002compoundhet | homalt | 99.8228 | 99.7344 | 99.9113 | 42.6999 | 3379 | 9 | 3380 | 3 | 2 | 66.6667 | |
| ciseli-custom | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 91.7959 | 97.7681 | 86.5114 | 40.4602 | 3373 | 77 | 3380 | 527 | 26 | 4.9336 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6097 | 95.8719 | 99.4116 | 60.6552 | 3414 | 147 | 3379 | 20 | 15 | 75.0000 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 41.1509 | 37.5633 | 45.4962 | 49.7904 | 2374 | 3946 | 3379 | 4048 | 3339 | 82.4852 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 41.1509 | 37.5633 | 45.4962 | 49.7904 | 2374 | 3946 | 3379 | 4048 | 3339 | 82.4852 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 81.9075 | 85.8815 | 78.2851 | 78.2609 | 3376 | 555 | 3378 | 937 | 16 | 1.7076 | |
| astatham-gatk | SNP | tv | HG002compoundhet | homalt | 99.8376 | 99.8524 | 99.8227 | 42.7314 | 3383 | 5 | 3378 | 6 | 5 | 83.3333 | |
| qzeng-custom | INDEL | I1_5 | * | hetalt | 84.6275 | 73.4792 | 99.7637 | 61.8865 | 8226 | 2969 | 3378 | 8 | 6 | 75.0000 | |
| mlin-fermikit | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 98.1542 | 97.8551 | 98.4553 | 37.1727 | 3376 | 74 | 3378 | 53 | 35 | 66.0377 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 84.3679 | 93.1480 | 77.1005 | 68.0245 | 3317 | 244 | 3377 | 1003 | 177 | 17.6471 | |
| jlack-gatk | SNP | tv | HG002compoundhet | homalt | 99.7638 | 99.8229 | 99.7048 | 42.2900 | 3382 | 6 | 3377 | 10 | 9 | 90.0000 | |
| rpoplin-dv42 | SNP | tv | HG002compoundhet | homalt | 99.7491 | 99.8229 | 99.6753 | 42.8668 | 3382 | 6 | 3377 | 11 | 9 | 81.8182 | |
| gduggal-bwafb | SNP | tv | HG002compoundhet | homalt | 99.1913 | 99.5573 | 98.8280 | 47.3709 | 3373 | 15 | 3373 | 40 | 33 | 82.5000 | |
| ciseli-custom | SNP | * | map_l150_m0_e0 | homalt | 84.0715 | 82.7097 | 85.4790 | 75.1182 | 3382 | 707 | 3373 | 573 | 459 | 80.1047 | |
| gduggal-bwafb | INDEL | I16_PLUS | * | * | 66.2146 | 51.1369 | 93.9014 | 38.2990 | 3261 | 3116 | 3372 | 219 | 218 | 99.5434 | |
| jmaeng-gatk | INDEL | * | HG002complexvar | hetalt | 91.1572 | 85.1041 | 98.1374 | 66.7119 | 3148 | 551 | 3372 | 64 | 64 | 100.0000 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.0919 | 98.8333 | 99.3518 | 73.8158 | 2965 | 35 | 3372 | 22 | 17 | 77.2727 | |
| anovak-vg | SNP | ti | map_l125_m0_e0 | homalt | 86.0648 | 75.9296 | 99.3223 | 69.5933 | 3410 | 1081 | 3371 | 23 | 21 | 91.3043 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.0392 | 94.3279 | 99.9110 | 42.3116 | 3326 | 200 | 3366 | 3 | 3 | 100.0000 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.0392 | 94.3279 | 99.9110 | 42.3116 | 3326 | 200 | 3366 | 3 | 3 | 100.0000 | |
| anovak-vg | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 81.1375 | 80.9173 | 81.3588 | 37.8886 | 3299 | 778 | 3365 | 771 | 561 | 72.7626 | |
| egarrison-hhga | SNP | tv | HG002compoundhet | homalt | 99.1596 | 99.2326 | 99.0866 | 43.1871 | 3362 | 26 | 3363 | 31 | 28 | 90.3226 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.9285 | 91.4672 | 96.5260 | 44.7581 | 879 | 82 | 3362 | 121 | 110 | 90.9091 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.1710 | 86.1140 | 99.1445 | 49.6360 | 3293 | 531 | 3361 | 29 | 28 | 96.5517 | |