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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
3451-3500 / 86044 show all | |||||||||||||||
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 90.6005 | 89.5230 | 91.7043 | 43.8461 | 16346 | 1913 | 17079 | 1545 | 1043 | 67.5081 | |
| mlin-fermikit | SNP | tv | map_l150_m2_e0 | homalt | 60.3616 | 53.1472 | 69.8423 | 60.3244 | 2170 | 1913 | 2170 | 937 | 869 | 92.7428 | |
| qzeng-custom | SNP | tv | map_l125_m0_e0 | * | 81.4498 | 71.1657 | 95.2082 | 88.9716 | 4719 | 1912 | 4709 | 237 | 201 | 84.8101 | |
| gduggal-bwaplat | SNP | tv | map_l250_m2_e0 | * | 50.3112 | 33.6572 | 99.5893 | 97.7433 | 970 | 1912 | 970 | 4 | 1 | 25.0000 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 62.0445 | 67.3110 | 57.5423 | 47.2192 | 3935 | 1911 | 5947 | 4388 | 3469 | 79.0565 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 62.0445 | 67.3110 | 57.5423 | 47.2192 | 3935 | 1911 | 5947 | 4388 | 3469 | 79.0565 | |
| qzeng-custom | SNP | ti | map_l250_m2_e1 | * | 74.5851 | 62.3719 | 92.7460 | 95.5643 | 3166 | 1910 | 3158 | 247 | 208 | 84.2105 | |
| anovak-vg | SNP | ti | map_l125_m2_e0 | het | 77.5170 | 89.8919 | 68.1370 | 78.1191 | 16968 | 1908 | 16853 | 7881 | 1719 | 21.8120 | |
| gduggal-snapvard | INDEL | D16_PLUS | * | hetalt | 0.0000 | 1.3451 | 0.0000 | 0.0000 | 26 | 1907 | 0 | 0 | 0 | ||
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 0.0000 | 1.3465 | 0.0000 | 0.0000 | 26 | 1905 | 0 | 0 | 0 | ||
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 0.0000 | 1.3465 | 0.0000 | 0.0000 | 26 | 1905 | 0 | 0 | 0 | ||
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.1122 | 95.6040 | 96.6259 | 60.2914 | 41430 | 1905 | 41238 | 1440 | 1303 | 90.4861 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 90.2790 | 82.8456 | 99.1780 | 30.0661 | 9200 | 1905 | 2413 | 20 | 17 | 85.0000 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 2.8165 | 1.5003 | 22.9630 | 60.5263 | 29 | 1904 | 31 | 104 | 70 | 67.3077 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 58.3043 | 52.2088 | 66.0112 | 56.8516 | 2080 | 1904 | 2249 | 1158 | 1030 | 88.9465 | |
| gduggal-snapplat | SNP | ti | map_l150_m2_e0 | * | 93.1515 | 90.7274 | 95.7087 | 84.4902 | 18610 | 1902 | 18623 | 835 | 473 | 56.6467 | |
| gduggal-snapvard | INDEL | D16_PLUS | HG002compoundhet | hetalt | 0.0000 | 1.3485 | 0.0000 | 0.0000 | 26 | 1902 | 0 | 0 | 0 | ||
| gduggal-snapfb | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 79.1493 | 72.0787 | 87.7579 | 53.3974 | 4910 | 1902 | 638 | 89 | 89 | 100.0000 | |
| gduggal-snapfb | SNP | ti | HG002complexvar | * | 99.2700 | 99.6259 | 98.9167 | 19.8956 | 506535 | 1902 | 507043 | 5553 | 819 | 14.7488 | |
| raldana-dualsentieon | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.6413 | 97.9883 | 99.3029 | 72.0487 | 92549 | 1900 | 92457 | 649 | 588 | 90.6009 | |
| ckim-dragen | INDEL | * | * | hetalt | 95.9597 | 92.4793 | 99.7124 | 57.0557 | 23339 | 1898 | 23575 | 68 | 68 | 100.0000 | |
| raldana-dualsentieon | INDEL | * | * | het | 99.3035 | 99.0228 | 99.5858 | 57.9096 | 192236 | 1897 | 191867 | 798 | 611 | 76.5664 | |
| gduggal-bwavard | SNP | * | map_l100_m2_e0 | * | 96.4651 | 97.4352 | 95.5142 | 75.4124 | 72067 | 1897 | 71074 | 3338 | 242 | 7.2499 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 83.7908 | 73.3408 | 97.7136 | 42.2636 | 5216 | 1896 | 5214 | 122 | 120 | 98.3607 | |
| qzeng-custom | SNP | ti | map_l250_m2_e0 | * | 74.3996 | 62.1406 | 92.6844 | 95.5558 | 3112 | 1896 | 3104 | 245 | 206 | 84.0816 | |
| anovak-vg | INDEL | D1_5 | HG002complexvar | het | 92.0015 | 90.8693 | 93.1622 | 52.9821 | 18869 | 1896 | 19565 | 1436 | 834 | 58.0780 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.8420 | 95.6294 | 98.0857 | 58.9442 | 41441 | 1894 | 41248 | 805 | 768 | 95.4037 | |
| jmaeng-gatk | SNP | ti | map_l150_m0_e0 | het | 76.1038 | 62.8605 | 96.4167 | 93.5560 | 3204 | 1893 | 3202 | 119 | 16 | 13.4454 | |
| ckim-isaac | SNP | * | HG002compoundhet | homalt | 90.1933 | 82.4430 | 99.5521 | 29.8507 | 8889 | 1893 | 8890 | 40 | 35 | 87.5000 | |
| gduggal-snapplat | SNP | ti | map_l150_m1_e0 | * | 92.9132 | 90.4018 | 95.5681 | 83.3799 | 17820 | 1892 | 17833 | 827 | 469 | 56.7110 | |
| gduggal-bwaplat | SNP | ti | map_l250_m2_e1 | het | 59.7244 | 42.6796 | 99.4358 | 97.5469 | 1408 | 1891 | 1410 | 8 | 2 | 25.0000 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 47.7195 | 36.5649 | 68.6675 | 29.6562 | 1090 | 1891 | 4370 | 1994 | 1989 | 99.7492 | |
| mlin-fermikit | SNP | tv | map_l150_m1_e0 | homalt | 59.5283 | 52.1287 | 69.3761 | 55.9108 | 2057 | 1889 | 2057 | 908 | 841 | 92.6211 | |
| ckim-dragen | INDEL | * | HG002compoundhet | hetalt | 96.0007 | 92.5060 | 99.7699 | 50.0702 | 23293 | 1887 | 23417 | 54 | 54 | 100.0000 | |
| gduggal-bwaplat | SNP | * | map_l250_m2_e1 | homalt | 46.8732 | 30.6107 | 100.0000 | 95.5861 | 832 | 1886 | 831 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 93.0896 | 87.2376 | 99.7831 | 59.6058 | 12885 | 1885 | 12884 | 28 | 19 | 67.8571 | |
| hfeng-pmm3 | SNP | * | * | het | 99.9317 | 99.8994 | 99.9639 | 18.5779 | 1871702 | 1885 | 1871578 | 675 | 30 | 4.4444 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 64.9017 | 48.2133 | 99.2588 | 53.0137 | 1754 | 1884 | 1741 | 13 | 10 | 76.9231 | |
| bgallagher-sentieon | INDEL | * | * | hetalt | 95.9976 | 92.5387 | 99.7251 | 56.9311 | 23354 | 1883 | 23582 | 65 | 64 | 98.4615 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 93.2644 | 90.8623 | 95.7970 | 33.1527 | 18714 | 1882 | 18667 | 819 | 734 | 89.6215 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 48.1828 | 41.3707 | 57.6805 | 50.9762 | 1328 | 1882 | 1318 | 967 | 944 | 97.6215 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 27.2634 | 21.9826 | 35.8835 | 56.2500 | 530 | 1881 | 530 | 947 | 929 | 98.0993 | |
| ckim-isaac | SNP | ti | HG002compoundhet | het | 88.4015 | 80.2104 | 98.4558 | 36.9008 | 7624 | 1881 | 7906 | 124 | 19 | 15.3226 | |
| ckim-gatk | SNP | ti | map_l150_m0_e0 | het | 76.3401 | 63.1156 | 96.5755 | 93.3356 | 3217 | 1880 | 3215 | 114 | 18 | 15.7895 | |
| qzeng-custom | SNP | tv | map_l150_m2_e1 | het | 83.6864 | 74.4284 | 95.5746 | 89.7620 | 5469 | 1879 | 5464 | 253 | 208 | 82.2134 | |
| eyeh-varpipe | INDEL | I16_PLUS | * | hetalt | 18.8152 | 10.4862 | 91.4634 | 56.9177 | 220 | 1878 | 225 | 21 | 21 | 100.0000 | |
| gduggal-snapvard | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 25.8158 | 15.0294 | 91.4439 | 71.5156 | 332 | 1877 | 342 | 32 | 20 | 62.5000 | |
| asubramanian-gatk | INDEL | * | * | hetalt | 95.6373 | 92.5665 | 98.9188 | 59.3274 | 23361 | 1876 | 23605 | 258 | 236 | 91.4729 | |
| bgallagher-sentieon | INDEL | * | HG002compoundhet | hetalt | 96.0304 | 92.5536 | 99.7785 | 50.2300 | 23305 | 1875 | 23427 | 52 | 52 | 100.0000 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 58.9132 | 46.9890 | 78.9474 | 83.7848 | 1662 | 1875 | 1725 | 460 | 86 | 18.6957 | |