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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
83501-83550 / 86044 show all | |||||||||||||||
| anovak-vg | INDEL | * | segdup | * | 73.2929 | 72.4961 | 74.1075 | 94.2874 | 1853 | 703 | 1889 | 660 | 536 | 81.2121 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 94.8741 | 95.6080 | 94.1515 | 50.7143 | 2351 | 108 | 9160 | 569 | 536 | 94.2004 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 67.4740 | 66.1145 | 68.8906 | 60.7168 | 2634 | 1350 | 2726 | 1231 | 537 | 43.6231 | |
| ciseli-custom | SNP | tv | map_l125_m2_e0 | * | 79.3554 | 74.4800 | 84.9139 | 78.4079 | 12281 | 4208 | 12276 | 2181 | 537 | 24.6217 | |
| gduggal-snapfb | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 88.4732 | 99.0329 | 79.9484 | 69.7226 | 55093 | 538 | 55477 | 13914 | 538 | 3.8666 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 51.6769 | 55.4825 | 48.3599 | 47.7729 | 506 | 406 | 516 | 551 | 538 | 97.6407 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.2571 | 98.0815 | 98.4334 | 52.3164 | 35890 | 702 | 35814 | 570 | 538 | 94.3860 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 46.1155 | 32.1540 | 81.5062 | 55.9877 | 2690 | 5676 | 2684 | 609 | 538 | 88.3415 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 49.7249 | 53.1915 | 46.6825 | 69.1220 | 400 | 352 | 591 | 675 | 539 | 79.8519 | |
| gduggal-snapplat | INDEL | D6_15 | * | * | 49.9163 | 35.9727 | 81.5114 | 64.7243 | 9386 | 16706 | 8068 | 1830 | 539 | 29.4536 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 51.3798 | 36.1160 | 88.9898 | 58.0399 | 4971 | 8793 | 4995 | 618 | 540 | 87.3786 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 91.0906 | 96.0483 | 86.6196 | 46.4616 | 2625 | 108 | 7477 | 1155 | 540 | 46.7532 | |
| jlack-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.6377 | 99.1486 | 98.1322 | 75.2542 | 47860 | 411 | 47652 | 907 | 540 | 59.5369 | |
| ciseli-custom | SNP | tv | map_l125_m2_e1 | * | 79.4183 | 74.5632 | 84.9497 | 78.4301 | 12420 | 4237 | 12412 | 2199 | 540 | 24.5566 | |
| ckim-dragen | INDEL | I1_5 | * | * | 99.2774 | 99.1830 | 99.3720 | 58.7161 | 149433 | 1231 | 149372 | 944 | 540 | 57.2034 | |
| anovak-vg | SNP | tv | map_l125_m0_e0 | * | 78.9708 | 83.7129 | 74.7373 | 81.6028 | 5551 | 1080 | 5547 | 1875 | 540 | 28.8000 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 94.7163 | 99.4919 | 90.3781 | 51.0003 | 5091 | 26 | 5091 | 542 | 540 | 99.6310 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 78.9597 | 78.8934 | 79.0261 | 42.0187 | 385 | 103 | 2061 | 547 | 541 | 98.9031 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.3553 | 99.7468 | 97.0021 | 67.1820 | 18120 | 46 | 18120 | 560 | 541 | 96.6071 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.3553 | 99.7468 | 97.0021 | 67.1820 | 18120 | 46 | 18120 | 560 | 541 | 96.6071 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 74.4014 | 87.0872 | 64.9416 | 71.9724 | 5591 | 829 | 6613 | 3570 | 542 | 15.1821 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 74.4014 | 87.0872 | 64.9416 | 71.9724 | 5591 | 829 | 6613 | 3570 | 542 | 15.1821 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 90.5202 | 96.8720 | 84.9501 | 59.2685 | 3066 | 99 | 3065 | 543 | 542 | 99.8158 | |
| ciseli-custom | SNP | ti | * | het | 97.9524 | 98.4710 | 97.4391 | 21.0644 | 1262297 | 19600 | 1259858 | 33111 | 542 | 1.6369 | |
| cchapple-custom | SNP | * | map_siren | het | 97.7546 | 98.5944 | 96.9290 | 63.2688 | 89712 | 1279 | 89826 | 2846 | 543 | 19.0794 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 76.4026 | 92.5078 | 65.0735 | 61.5548 | 889 | 72 | 1062 | 570 | 543 | 95.2632 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 21.5835 | 18.1202 | 26.6833 | 26.4895 | 214 | 967 | 214 | 588 | 544 | 92.5170 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 97.1108 | 97.1608 | 97.0609 | 55.5769 | 24639 | 720 | 24636 | 746 | 544 | 72.9223 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 77.9189 | 77.3944 | 78.4506 | 71.4753 | 2804 | 819 | 2876 | 790 | 545 | 68.9873 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 82.2424 | 75.3576 | 90.5117 | 53.1553 | 4584 | 1499 | 5590 | 586 | 545 | 93.0034 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 79.6057 | 84.7414 | 75.0569 | 26.8642 | 1655 | 298 | 1649 | 548 | 546 | 99.6350 | |
| gduggal-snapplat | SNP | * | map_l125_m0_e0 | * | 91.0834 | 87.8360 | 94.5802 | 84.8287 | 17027 | 2358 | 17032 | 976 | 546 | 55.9426 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 96.8247 | 99.2858 | 94.4828 | 49.5258 | 9453 | 68 | 9453 | 552 | 547 | 99.0942 | |
| jlack-gatk | SNP | * | * | * | 99.7200 | 99.9393 | 99.5016 | 23.6335 | 3052765 | 1854 | 3052612 | 15290 | 548 | 3.5840 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.0569 | 99.3663 | 91.1057 | 57.4139 | 5645 | 36 | 5644 | 551 | 548 | 99.4555 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 80.2615 | 74.0424 | 87.6212 | 52.2423 | 4504 | 1579 | 4339 | 613 | 548 | 89.3964 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 89.1325 | 94.2362 | 84.5533 | 48.1916 | 3646 | 223 | 3246 | 593 | 548 | 92.4115 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 91.7464 | 96.2737 | 87.6259 | 45.7712 | 3152 | 122 | 8703 | 1229 | 548 | 44.5891 | |
| qzeng-custom | SNP | * | map_l150_m1_e0 | het | 81.0937 | 70.5218 | 95.3942 | 89.4771 | 13622 | 5694 | 13504 | 652 | 548 | 84.0491 | |
| qzeng-custom | SNP | tv | * | * | 99.4379 | 99.2180 | 99.6588 | 26.4392 | 962115 | 7583 | 958619 | 3282 | 549 | 16.7276 | |
| rpoplin-dv42 | INDEL | D1_5 | * | * | 99.4429 | 99.3110 | 99.5751 | 58.2332 | 145734 | 1011 | 145779 | 622 | 549 | 88.2637 | |
| qzeng-custom | SNP | * | map_l150_m2_e0 | het | 81.6474 | 71.2611 | 95.5780 | 89.7912 | 14347 | 5786 | 14222 | 658 | 550 | 83.5866 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 75.3156 | 74.9046 | 75.7313 | 50.0285 | 2943 | 986 | 3314 | 1062 | 550 | 51.7891 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 51.1782 | 35.9607 | 88.7235 | 60.7545 | 5046 | 8986 | 5067 | 644 | 550 | 85.4037 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 57.0334 | 48.7504 | 68.7072 | 56.9745 | 1736 | 1825 | 1706 | 777 | 550 | 70.7851 | |
| cchapple-custom | SNP | * | map_siren | * | 98.2653 | 98.4743 | 98.0572 | 58.9696 | 143997 | 2231 | 143999 | 2853 | 550 | 19.2780 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.3939 | 98.8110 | 96.0169 | 66.9230 | 17950 | 216 | 18586 | 771 | 551 | 71.4656 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.3939 | 98.8110 | 96.0169 | 66.9230 | 17950 | 216 | 18586 | 771 | 551 | 71.4656 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 97.1231 | 96.5890 | 97.6631 | 54.5313 | 24494 | 865 | 24490 | 586 | 552 | 94.1980 | |
| jlack-gatk | INDEL | D1_5 | * | * | 99.0320 | 99.1134 | 98.9507 | 60.1218 | 145444 | 1301 | 145502 | 1543 | 552 | 35.7745 | |