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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
82901-82950 / 86044 show all | |||||||||||||||
| anovak-vg | SNP | ti | map_l250_m2_e1 | het | 72.2384 | 86.6323 | 61.9461 | 92.2704 | 2858 | 441 | 2852 | 1752 | 393 | 22.4315 | |
| astatham-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.9849 | 94.4009 | 95.5762 | 69.0899 | 9509 | 564 | 9355 | 433 | 393 | 90.7621 | |
| anovak-vg | INDEL | * | map_l125_m2_e1 | * | 72.6951 | 74.3371 | 71.1241 | 87.8885 | 1654 | 571 | 1702 | 691 | 393 | 56.8741 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.7571 | 99.7248 | 97.8080 | 67.5218 | 18116 | 50 | 18116 | 406 | 393 | 96.7980 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.7571 | 99.7248 | 97.8080 | 67.5218 | 18116 | 50 | 18116 | 406 | 393 | 96.7980 | |
| cchapple-custom | SNP | * | HG002complexvar | het | 99.7839 | 99.6872 | 99.8808 | 18.7433 | 464041 | 1456 | 463256 | 553 | 394 | 71.2477 | |
| anovak-vg | SNP | ti | map_l250_m2_e0 | * | 75.7617 | 82.2684 | 70.2088 | 91.5692 | 4120 | 888 | 4103 | 1741 | 394 | 22.6307 | |
| asubramanian-gatk | INDEL | D6_15 | HG002compoundhet | * | 94.5808 | 93.8213 | 95.3528 | 36.4670 | 8473 | 558 | 8474 | 413 | 394 | 95.3995 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 93.9385 | 90.7361 | 97.3752 | 52.7808 | 18022 | 1840 | 18957 | 511 | 394 | 77.1037 | |
| gduggal-snapplat | SNP | tv | map_l100_m1_e0 | het | 94.6299 | 94.5320 | 94.7279 | 81.7875 | 14574 | 843 | 14572 | 811 | 394 | 48.5820 | |
| gduggal-snapfb | SNP | * | map_l125_m0_e0 | * | 95.4423 | 95.2231 | 95.6625 | 77.2744 | 18459 | 926 | 18460 | 837 | 394 | 47.0729 | |
| gduggal-snapfb | SNP | ti | map_l125_m1_e0 | het | 96.3921 | 97.2572 | 95.5423 | 70.8639 | 17765 | 501 | 17768 | 829 | 394 | 47.5271 | |
| gduggal-snapfb | SNP | ti | map_l125_m2_e0 | het | 96.4670 | 97.3405 | 95.6090 | 72.9883 | 18374 | 502 | 18377 | 844 | 395 | 46.8009 | |
| gduggal-snapfb | SNP | ti | map_l125_m2_e1 | het | 96.4982 | 97.3699 | 95.6419 | 73.0724 | 18585 | 502 | 18588 | 847 | 395 | 46.6352 | |
| gduggal-snapplat | SNP | tv | map_l100_m2_e0 | het | 94.7121 | 94.6314 | 94.7930 | 82.9183 | 14930 | 847 | 14928 | 820 | 395 | 48.1707 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 91.0653 | 90.2147 | 91.9320 | 48.7934 | 10713 | 1162 | 10768 | 945 | 395 | 41.7989 | |
| ckim-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.7342 | 93.9641 | 95.5170 | 68.9673 | 9465 | 608 | 9311 | 437 | 395 | 90.3890 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 85.0825 | 75.8761 | 96.8314 | 49.6990 | 18620 | 5920 | 18611 | 609 | 395 | 64.8604 | |
| qzeng-custom | SNP | * | map_l150_m0_e0 | * | 75.4274 | 62.9239 | 94.1324 | 92.2685 | 7571 | 4461 | 7492 | 467 | 396 | 84.7966 | |
| raldana-dualsentieon | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.2233 | 91.0156 | 95.5407 | 66.1212 | 9168 | 905 | 9020 | 421 | 396 | 94.0618 | |
| ckim-dragen | INDEL | D1_5 | * | * | 99.4199 | 99.4105 | 99.4294 | 60.9956 | 145880 | 865 | 145840 | 837 | 396 | 47.3118 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 48.1114 | 83.3977 | 33.8073 | 56.3749 | 216 | 43 | 214 | 419 | 397 | 94.7494 | |
| gduggal-snapplat | SNP | tv | map_l100_m2_e1 | het | 94.7477 | 94.6794 | 94.8162 | 82.9388 | 15090 | 848 | 15090 | 825 | 397 | 48.1212 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 77.5652 | 94.8718 | 65.5987 | 55.1946 | 703 | 38 | 778 | 408 | 397 | 97.3039 | |
| ckim-vqsr | INDEL | I1_5 | * | * | 99.3579 | 99.0515 | 99.6662 | 59.3791 | 149235 | 1429 | 149282 | 500 | 397 | 79.4000 | |
| anovak-vg | INDEL | I1_5 | segdup | * | 58.1085 | 58.4514 | 57.7697 | 94.2442 | 619 | 440 | 632 | 462 | 397 | 85.9307 | |
| bgallagher-sentieon | INDEL | D1_5 | * | * | 99.5437 | 99.4494 | 99.6383 | 60.2111 | 145937 | 808 | 145993 | 530 | 397 | 74.9057 | |
| anovak-vg | SNP | ti | map_l250_m2_e1 | * | 75.8245 | 82.3089 | 70.2872 | 91.6096 | 4178 | 898 | 4161 | 1759 | 398 | 22.6265 | |
| ciseli-custom | INDEL | D16_PLUS | HG002complexvar | homalt | 50.2549 | 88.5813 | 35.0778 | 60.5689 | 256 | 33 | 248 | 459 | 398 | 86.7102 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 94.1229 | 98.2424 | 90.3349 | 66.0632 | 3801 | 68 | 3776 | 404 | 398 | 98.5149 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 82.5353 | 76.8626 | 89.1121 | 55.4494 | 3126 | 941 | 3282 | 401 | 398 | 99.2519 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 57.7607 | 47.6176 | 73.3945 | 69.4184 | 3198 | 3518 | 4720 | 1711 | 398 | 23.2613 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 58.8151 | 45.7510 | 82.3221 | 66.0165 | 2778 | 3294 | 3772 | 810 | 398 | 49.1358 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 74.6510 | 71.8045 | 77.7324 | 73.3424 | 1528 | 600 | 1522 | 436 | 398 | 91.2844 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 86.2248 | 91.8756 | 81.2289 | 81.5160 | 8391 | 742 | 8646 | 1998 | 399 | 19.9700 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 86.2248 | 91.8756 | 81.2289 | 81.5160 | 8391 | 742 | 8646 | 1998 | 399 | 19.9700 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.1835 | 98.9169 | 97.4610 | 70.8771 | 17626 | 193 | 17235 | 449 | 399 | 88.8641 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.5003 | 96.1325 | 98.9076 | 58.5444 | 41659 | 1676 | 41469 | 458 | 399 | 87.1179 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 20.1055 | 12.5225 | 50.9714 | 65.7132 | 488 | 3409 | 446 | 429 | 399 | 93.0070 | |
| ciseli-custom | SNP | tv | map_l150_m2_e0 | * | 76.6548 | 71.4839 | 82.6322 | 82.1021 | 8117 | 3238 | 8112 | 1705 | 399 | 23.4018 | |
| gduggal-snapfb | SNP | * | HG002complexvar | homalt | 99.5552 | 99.6857 | 99.4250 | 21.2913 | 287668 | 907 | 287733 | 1664 | 399 | 23.9784 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 68.6915 | 87.3964 | 56.5817 | 68.5791 | 527 | 76 | 533 | 409 | 399 | 97.5550 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 78.8211 | 67.4076 | 94.8874 | 32.5021 | 2608 | 1261 | 7628 | 411 | 399 | 97.0803 | |
| gduggal-snapvard | INDEL | C1_5 | * | * | 59.8991 | 90.0000 | 44.8865 | 88.9071 | 9 | 1 | 3125 | 3837 | 400 | 10.4248 | |
| qzeng-custom | SNP | ti | HG002complexvar | * | 99.1315 | 98.4529 | 99.8194 | 18.2769 | 500571 | 7866 | 493623 | 893 | 400 | 44.7928 | |
| gduggal-snapfb | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 78.2170 | 70.8374 | 87.3129 | 79.9686 | 10921 | 4496 | 3792 | 551 | 400 | 72.5953 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.6446 | 98.9272 | 98.3637 | 73.5579 | 30153 | 327 | 29696 | 494 | 401 | 81.1741 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.6446 | 98.9272 | 98.3637 | 73.5579 | 30153 | 327 | 29696 | 494 | 401 | 81.1741 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 91.6770 | 95.2628 | 88.3513 | 55.6869 | 1468 | 73 | 6227 | 821 | 401 | 48.8429 | |
| ckim-isaac | SNP | tv | HG002complexvar | * | 95.4727 | 91.5159 | 99.7871 | 19.3101 | 225271 | 20884 | 225437 | 481 | 401 | 83.3680 | |