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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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82801-82850 / 86044 show all | |||||||||||||||
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 51.9214 | 45.2924 | 60.8234 | 54.7022 | 1270 | 1534 | 1374 | 885 | 630 | 71.1864 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.3184 | 96.2571 | 98.4034 | 52.4797 | 41713 | 1622 | 54546 | 885 | 782 | 88.3616 | |
| ciseli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 91.8329 | 98.7645 | 85.8105 | 79.7572 | 5356 | 67 | 5352 | 885 | 251 | 28.3616 | |
| ciseli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 91.8329 | 98.7645 | 85.8105 | 79.7572 | 5356 | 67 | 5352 | 885 | 251 | 28.3616 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 72.8517 | 89.6171 | 61.3706 | 74.5275 | 1381 | 160 | 1406 | 885 | 863 | 97.5141 | |
| anovak-vg | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 43.8638 | 34.2213 | 61.0721 | 38.4199 | 167 | 321 | 1390 | 886 | 815 | 91.9865 | |
| mlin-fermikit | SNP | * | map_l150_m0_e0 | homalt | 52.6207 | 43.4581 | 66.6792 | 59.8524 | 1777 | 2312 | 1777 | 888 | 815 | 91.7793 | |
| ndellapenna-hhga | SNP | ti | * | * | 99.8903 | 99.8233 | 99.9574 | 16.8793 | 2081825 | 3686 | 2081847 | 888 | 298 | 33.5586 | |
| dgrover-gatk | INDEL | * | * | het | 99.5990 | 99.6559 | 99.5422 | 61.2168 | 193465 | 668 | 193091 | 888 | 555 | 62.5000 | |
| cchapple-custom | SNP | tv | map_l100_m2_e0 | * | 97.1975 | 97.9028 | 96.5023 | 71.7198 | 24508 | 525 | 24500 | 888 | 133 | 14.9775 | |
| cchapple-custom | SNP | tv | map_l100_m2_e0 | het | 96.2979 | 98.0731 | 94.5857 | 75.5847 | 15473 | 304 | 15513 | 888 | 133 | 14.9775 | |
| gduggal-snapvard | INDEL | * | map_l100_m1_e0 | het | 84.8981 | 94.4519 | 77.0994 | 87.8634 | 2111 | 124 | 2993 | 889 | 409 | 46.0067 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.3372 | 98.5927 | 92.2897 | 84.7602 | 10649 | 152 | 10677 | 892 | 112 | 12.5561 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 47.8556 | 54.0432 | 42.9393 | 43.9068 | 675 | 574 | 672 | 893 | 863 | 96.6405 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 47.8556 | 54.0432 | 42.9393 | 43.9068 | 675 | 574 | 672 | 893 | 863 | 96.6405 | |
| qzeng-custom | SNP | ti | HG002complexvar | * | 99.1315 | 98.4529 | 99.8194 | 18.2769 | 500571 | 7866 | 493623 | 893 | 400 | 44.7928 | |
| jpowers-varprowl | INDEL | I6_15 | HG002complexvar | * | 68.3061 | 61.4775 | 76.8413 | 54.9585 | 2946 | 1846 | 2963 | 893 | 875 | 97.9843 | |
| hfeng-pmm2 | INDEL | * | HG002compoundhet | * | 94.6829 | 92.5968 | 96.8651 | 60.5702 | 27742 | 2218 | 27624 | 894 | 877 | 98.0984 | |
| ghariani-varprowl | SNP | ti | map_l100_m2_e0 | * | 98.5956 | 99.0053 | 98.1892 | 70.8668 | 48474 | 487 | 48476 | 894 | 185 | 20.6935 | |
| gduggal-snapfb | SNP | tv | HG002complexvar | homalt | 99.3543 | 99.6457 | 99.0647 | 24.8993 | 94774 | 337 | 94793 | 895 | 159 | 17.7654 | |
| cchapple-custom | SNP | tv | map_l100_m2_e1 | * | 97.2075 | 97.9156 | 96.5096 | 71.7543 | 24756 | 527 | 24747 | 895 | 134 | 14.9721 | |
| cchapple-custom | SNP | tv | map_l100_m2_e1 | het | 96.3138 | 98.0926 | 94.5983 | 75.6213 | 15634 | 304 | 15674 | 895 | 134 | 14.9721 | |
| eyeh-varpipe | INDEL | D16_PLUS | * | homalt | 49.8532 | 50.8274 | 48.9155 | 43.2091 | 860 | 832 | 857 | 895 | 865 | 96.6480 | |
| eyeh-varpipe | INDEL | D6_15 | * | het | 91.9882 | 92.1325 | 91.8444 | 46.7075 | 10680 | 912 | 10079 | 895 | 860 | 96.0894 | |
| jlack-gatk | SNP | * | map_l250_m2_e0 | het | 91.0733 | 98.0169 | 85.0484 | 94.0579 | 5091 | 103 | 5091 | 895 | 58 | 6.4805 | |
| mlin-fermikit | INDEL | D1_5 | HG002complexvar | * | 96.3667 | 95.5494 | 97.1980 | 54.2316 | 31259 | 1456 | 31081 | 896 | 836 | 93.3036 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 65.5149 | 76.6385 | 57.2111 | 69.3456 | 1181 | 360 | 1198 | 896 | 886 | 98.8839 | |
| anovak-vg | INDEL | * | map_siren | het | 71.2155 | 65.8829 | 77.4874 | 82.2828 | 2970 | 1538 | 3084 | 896 | 298 | 33.2589 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 61.2783 | 55.3295 | 68.6604 | 44.0399 | 2040 | 1647 | 1963 | 896 | 675 | 75.3348 | |
| jpowers-varprowl | SNP | * | map_l125_m1_e0 | * | 97.5600 | 97.1209 | 98.0031 | 75.2469 | 44022 | 1305 | 44022 | 897 | 282 | 31.4381 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 49.3231 | 87.8558 | 34.2857 | 65.7723 | 463 | 64 | 468 | 897 | 893 | 99.5541 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 34.5930 | 24.0897 | 61.3362 | 63.5277 | 1429 | 4503 | 1423 | 897 | 832 | 92.7536 | |
| ghariani-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 63.7991 | 90.6900 | 49.2081 | 87.2696 | 828 | 85 | 870 | 898 | 2 | 0.2227 | |
| gduggal-snapvard | INDEL | C6_15 | * | het | 48.6270 | 100.0000 | 32.1240 | 84.8018 | 7 | 0 | 425 | 898 | 137 | 15.2561 | |
| eyeh-varpipe | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.1234 | 99.6134 | 96.6774 | 60.9972 | 27571 | 107 | 26129 | 898 | 85 | 9.4655 | |
| jpowers-varprowl | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.7629 | 99.8762 | 95.7372 | 62.6774 | 20174 | 25 | 20213 | 900 | 534 | 59.3333 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 4.4684 | 35.0877 | 2.3861 | 92.1778 | 20 | 37 | 22 | 900 | 12 | 1.3333 | |
| jpowers-varprowl | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 70.1373 | 58.7236 | 87.0583 | 47.6620 | 6082 | 4275 | 6061 | 901 | 793 | 88.0133 | |
| jlack-gatk | SNP | * | map_l250_m2_e1 | het | 91.1258 | 98.0243 | 85.1345 | 94.1114 | 5160 | 104 | 5160 | 901 | 60 | 6.6593 | |
| jlack-gatk | INDEL | D6_15 | * | * | 96.4774 | 96.4127 | 96.5422 | 54.8116 | 25156 | 936 | 25156 | 901 | 581 | 64.4839 | |
| ckim-isaac | INDEL | D1_5 | HG002complexvar | * | 94.1980 | 91.4993 | 97.0606 | 47.3235 | 29934 | 2781 | 29752 | 901 | 456 | 50.6104 | |
| ghariani-varprowl | SNP | ti | map_l100_m2_e1 | * | 98.6004 | 99.0118 | 98.1924 | 70.8832 | 48996 | 489 | 48998 | 902 | 186 | 20.6208 | |
| gduggal-snapplat | INDEL | D1_5 | HG002complexvar | homalt | 88.1224 | 84.5537 | 92.0057 | 61.9576 | 8961 | 1637 | 10381 | 902 | 472 | 52.3282 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 51.7650 | 93.7381 | 35.7550 | 67.8055 | 494 | 33 | 502 | 902 | 894 | 99.1131 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 81.2248 | 74.4026 | 89.4244 | 27.1457 | 7037 | 2421 | 7644 | 904 | 893 | 98.7832 | |
| jpowers-varprowl | INDEL | D6_15 | HG002complexvar | het | 82.3223 | 90.1603 | 75.7381 | 57.2412 | 2813 | 307 | 2822 | 904 | 873 | 96.5708 | |
| jmaeng-gatk | INDEL | * | HG002compoundhet | homalt | 60.0968 | 99.5627 | 43.0372 | 84.8886 | 683 | 3 | 683 | 904 | 898 | 99.3363 | |
| ciseli-custom | SNP | ti | map_l150_m0_e0 | het | 72.0997 | 66.3920 | 78.8811 | 87.9805 | 3384 | 1713 | 3384 | 906 | 29 | 3.2009 | |
| ckim-vqsr | INDEL | * | * | het | 99.5204 | 99.5086 | 99.5323 | 62.3713 | 193179 | 954 | 192796 | 906 | 561 | 61.9205 | |
| jlack-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.6377 | 99.1486 | 98.1322 | 75.2542 | 47860 | 411 | 47652 | 907 | 540 | 59.5369 | |