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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
5801-5850 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | INDEL | * | HG002complexvar | hetalt | 86.5340 | 77.9941 | 97.1740 | 71.6888 | 2885 | 814 | 2854 | 83 | 75 | 90.3614 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 75.1577 | 77.7747 | 72.7110 | 36.3946 | 2845 | 813 | 4074 | 1529 | 1142 | 74.6893 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 81.6150 | 69.6868 | 98.4699 | 49.2653 | 1869 | 813 | 1802 | 28 | 24 | 85.7143 | |
| asubramanian-gatk | SNP | tv | map_l250_m2_e1 | homalt | 24.8148 | 14.1649 | 100.0000 | 97.9315 | 134 | 812 | 134 | 0 | 0 | ||
| jpowers-varprowl | SNP | tv | map_siren | * | 98.2043 | 98.2321 | 98.1765 | 64.5026 | 45118 | 812 | 45118 | 838 | 186 | 22.1957 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9638 | 97.4619 | 98.4709 | 54.8834 | 31180 | 812 | 31104 | 483 | 468 | 96.8944 | |
| ckim-dragen | INDEL | I1_5 | HG002compoundhet | * | 94.8982 | 93.4283 | 96.4151 | 65.5477 | 11544 | 812 | 11538 | 429 | 425 | 99.0676 | |
| hfeng-pmm3 | INDEL | D6_15 | * | * | 98.0738 | 96.8879 | 99.2891 | 51.0206 | 25280 | 812 | 25279 | 181 | 162 | 89.5028 | |
| jpowers-varprowl | SNP | * | map_l150_m1_e0 | het | 96.1124 | 95.8014 | 96.4254 | 81.4447 | 18505 | 811 | 18505 | 686 | 205 | 29.8834 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 81.8304 | 69.7614 | 98.9490 | 45.2532 | 1871 | 811 | 1883 | 20 | 20 | 100.0000 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.4367 | 96.0623 | 98.8510 | 34.0969 | 19785 | 811 | 20562 | 239 | 223 | 93.3054 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 68.4973 | 52.5761 | 98.2495 | 47.4411 | 898 | 810 | 898 | 16 | 15 | 93.7500 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 69.9678 | 56.0261 | 93.1470 | 80.3055 | 1032 | 810 | 1033 | 76 | 17 | 22.3684 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 46.7905 | 38.6828 | 59.1981 | 64.3248 | 511 | 810 | 502 | 346 | 329 | 95.0867 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 46.9083 | 32.3849 | 85.0498 | 32.2072 | 387 | 808 | 256 | 45 | 39 | 86.6667 | |
| ckim-gatk | SNP | tv | HG002complexvar | het | 99.7094 | 99.4639 | 99.9560 | 22.1876 | 149923 | 808 | 149845 | 66 | 19 | 28.7879 | |
| ltrigg-rtg1 | INDEL | * | HG002complexvar | het | 98.9136 | 98.2515 | 99.5847 | 53.0906 | 45404 | 808 | 44604 | 186 | 79 | 42.4731 | |
| bgallagher-sentieon | INDEL | D1_5 | * | * | 99.5437 | 99.4494 | 99.6383 | 60.2111 | 145937 | 808 | 145993 | 530 | 397 | 74.9057 | |
| gduggal-snapplat | SNP | ti | map_l250_m2_e0 | * | 88.7392 | 83.8658 | 94.2139 | 93.6830 | 4200 | 808 | 4201 | 258 | 136 | 52.7132 | |
| gduggal-snapplat | SNP | * | map_l250_m2_e0 | het | 87.7154 | 84.4628 | 91.2284 | 94.8727 | 4387 | 807 | 4389 | 422 | 202 | 47.8673 | |
| jlack-gatk | INDEL | D6_15 | HG002compoundhet | * | 92.1390 | 91.0641 | 93.2396 | 35.4470 | 8224 | 807 | 8220 | 596 | 552 | 92.6174 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 0.0000 | 7.4541 | 0.0000 | 0.0000 | 65 | 807 | 0 | 0 | 0 | ||
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 0.0000 | 85.1600 | 0.0000 | 0.0000 | 4631 | 807 | 0 | 0 | 0 | ||
| rpoplin-dv42 | INDEL | I6_15 | * | hetalt | 94.8036 | 90.5625 | 99.4614 | 37.3252 | 7744 | 807 | 7756 | 42 | 40 | 95.2381 | |
| rpoplin-dv42 | INDEL | I6_15 | HG002compoundhet | hetalt | 95.0099 | 90.5470 | 99.9355 | 28.7042 | 7730 | 807 | 7742 | 5 | 5 | 100.0000 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 66.1516 | 85.8124 | 53.8205 | 46.0515 | 4875 | 806 | 4846 | 4158 | 3808 | 91.5825 | |
| ltrigg-rtg1 | INDEL | I6_15 | * | hetalt | 94.9898 | 90.5742 | 99.8580 | 43.9696 | 7745 | 806 | 7738 | 11 | 10 | 90.9091 | |
| asubramanian-gatk | SNP | tv | map_l250_m2_e0 | homalt | 24.5318 | 13.9808 | 100.0000 | 97.9454 | 131 | 806 | 131 | 0 | 0 | ||
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 27.6970 | 19.6607 | 46.8447 | 68.8822 | 197 | 805 | 193 | 219 | 209 | 95.4338 | |
| jmaeng-gatk | SNP | tv | map_l250_m2_e1 | het | 72.8186 | 59.0331 | 95.0041 | 96.9764 | 1160 | 805 | 1160 | 61 | 1 | 1.6393 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | * | * | 92.6024 | 87.3765 | 98.4933 | 47.8680 | 5572 | 805 | 5491 | 84 | 71 | 84.5238 | |
| gduggal-snapplat | INDEL | D1_5 | HG002complexvar | hetalt | 53.4943 | 40.5325 | 78.6432 | 87.0210 | 548 | 804 | 626 | 170 | 133 | 78.2353 | |
| gduggal-snapvard | SNP | ti | map_l150_m2_e1 | * | 92.6900 | 96.1203 | 89.4961 | 82.4891 | 19919 | 804 | 19733 | 2316 | 191 | 8.2470 | |
| ltrigg-rtg1 | INDEL | I6_15 | HG002compoundhet | hetalt | 95.0169 | 90.5822 | 99.9083 | 29.3644 | 7733 | 804 | 7628 | 7 | 6 | 85.7143 | |
| hfeng-pmm3 | SNP | tv | * | * | 99.9443 | 99.9171 | 99.9715 | 21.1004 | 968886 | 804 | 968804 | 276 | 31 | 11.2319 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.1334 | 94.7850 | 99.6011 | 59.6178 | 14613 | 804 | 14733 | 59 | 58 | 98.3051 | |
| hfeng-pmm2 | INDEL | D6_15 | * | * | 98.0668 | 96.9186 | 99.2426 | 51.7103 | 25288 | 804 | 25288 | 193 | 170 | 88.0829 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 31.9797 | 0.0000 | 0.0000 | 378 | 804 | 0 | 0 | 0 | ||
| astatham-gatk | SNP | tv | map_l125_m0_e0 | * | 93.2991 | 87.8751 | 99.4368 | 79.1316 | 5827 | 804 | 5826 | 33 | 9 | 27.2727 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.8059 | 94.1587 | 99.6062 | 31.3760 | 12960 | 804 | 13154 | 52 | 51 | 98.0769 | |
| gduggal-snapvard | INDEL | D1_5 | HG002complexvar | het | 89.8124 | 96.1325 | 84.2721 | 56.4465 | 19960 | 803 | 25510 | 4761 | 3355 | 70.4684 | |
| ckim-gatk | SNP | tv | map_l250_m2_e1 | het | 72.9840 | 59.1858 | 95.1718 | 96.8842 | 1163 | 802 | 1163 | 59 | 1 | 1.6949 | |
| ckim-vqsr | INDEL | I6_15 | * | * | 97.6524 | 96.7691 | 98.5520 | 52.9508 | 24021 | 802 | 24026 | 353 | 331 | 93.7677 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.9671 | 94.1821 | 95.7654 | 49.5027 | 12983 | 802 | 12981 | 574 | 528 | 91.9861 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 23.8291 | 16.6493 | 41.8960 | 68.3446 | 160 | 801 | 137 | 190 | 58 | 30.5263 | |
| eyeh-varpipe | INDEL | I6_15 | HG002complexvar | hetalt | 50.4268 | 34.5053 | 93.6293 | 59.7826 | 422 | 801 | 485 | 33 | 33 | 100.0000 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 57.3590 | 53.6994 | 61.5538 | 40.3800 | 929 | 801 | 927 | 579 | 570 | 98.4456 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 93.1476 | 88.3677 | 98.4741 | 26.6190 | 6085 | 801 | 6260 | 97 | 90 | 92.7835 | |
| jmaeng-gatk | SNP | tv | map_l250_m2_e0 | het | 72.5709 | 58.7113 | 94.9958 | 96.9665 | 1139 | 801 | 1139 | 60 | 1 | 1.6667 | |
| ndellapenna-hhga | SNP | ti | map_siren | * | 99.5376 | 99.2028 | 99.8746 | 51.9628 | 99555 | 800 | 99557 | 125 | 60 | 48.0000 | |