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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
2001-2050 / 86044 show all | |||||||||||||||
| anovak-vg | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 32.9741 | 0.0000 | 0.0000 | 1958 | 3980 | 0 | 0 | 0 | ||
| cchapple-custom | INDEL | * | * | * | 99.1388 | 98.8448 | 99.4346 | 57.2260 | 340562 | 3980 | 363520 | 2067 | 1592 | 77.0198 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 61.3722 | 45.0807 | 96.1020 | 31.7355 | 3267 | 3980 | 3353 | 136 | 135 | 99.2647 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 62.7686 | 68.2214 | 58.1230 | 35.1882 | 8542 | 3979 | 16951 | 12213 | 9571 | 78.3673 | |
| gduggal-bwaplat | SNP | ti | map_l125_m0_e0 | het | 68.0749 | 51.8819 | 98.9622 | 92.4159 | 4287 | 3976 | 4291 | 45 | 14 | 31.1111 | |
| gduggal-bwaplat | SNP | tv | map_l100_m2_e0 | het | 85.2808 | 74.8051 | 99.1683 | 86.8061 | 11802 | 3975 | 11804 | 99 | 19 | 19.1919 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 44.4338 | 30.6874 | 80.4889 | 73.3333 | 1759 | 3973 | 1745 | 423 | 294 | 69.5035 | |
| anovak-vg | SNP | ti | map_l125_m2_e1 | * | 81.5574 | 87.0097 | 76.7480 | 75.9636 | 26598 | 3971 | 26376 | 7991 | 1774 | 22.2000 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 83.5380 | 73.1417 | 97.3796 | 64.9640 | 10814 | 3971 | 10814 | 291 | 228 | 78.3505 | |
| gduggal-bwaplat | SNP | tv | map_l100_m1_e0 | het | 84.9313 | 74.2687 | 99.1687 | 85.9377 | 11450 | 3967 | 11452 | 96 | 19 | 19.7917 | |
| jmaeng-gatk | SNP | * | HG002complexvar | homalt | 99.3008 | 98.6263 | 99.9845 | 20.0307 | 284610 | 3964 | 284586 | 44 | 39 | 88.6364 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 0.0000 | 27.1056 | 0.0000 | 0.0000 | 1474 | 3964 | 0 | 0 | 0 | ||
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 4.7196 | 2.6063 | 24.9453 | 76.2474 | 106 | 3961 | 114 | 343 | 228 | 66.4723 | |
| anovak-vg | SNP | ti | map_l125_m2_e0 | * | 81.4788 | 86.9291 | 76.6717 | 75.9478 | 26303 | 3955 | 26086 | 7937 | 1770 | 22.3006 | |
| qzeng-custom | SNP | ti | map_l150_m2_e1 | het | 80.5961 | 69.6581 | 95.6089 | 89.9144 | 9066 | 3949 | 9036 | 415 | 349 | 84.0964 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 41.1509 | 37.5633 | 45.4962 | 49.7904 | 2374 | 3946 | 3379 | 4048 | 3339 | 82.4852 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 41.1509 | 37.5633 | 45.4962 | 49.7904 | 2374 | 3946 | 3379 | 4048 | 3339 | 82.4852 | |
| ckim-gatk | SNP | ti | HG002complexvar | * | 99.5943 | 99.2243 | 99.9671 | 17.9110 | 504492 | 3944 | 504432 | 166 | 74 | 44.5783 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 89.5433 | 87.3487 | 91.8510 | 85.8019 | 27203 | 3940 | 27288 | 2421 | 244 | 10.0785 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 89.5433 | 87.3487 | 91.8510 | 85.8019 | 27203 | 3940 | 27288 | 2421 | 244 | 10.0785 | |
| qzeng-custom | SNP | * | HG002complexvar | homalt | 99.2256 | 98.6350 | 99.8233 | 20.2251 | 284636 | 3939 | 274538 | 486 | 380 | 78.1893 | |
| qzeng-custom | SNP | tv | map_siren | het | 91.9469 | 86.2561 | 98.4416 | 72.2639 | 24677 | 3932 | 24636 | 390 | 264 | 67.6923 | |
| ndellapenna-hhga | INDEL | D1_5 | HG002compoundhet | * | 69.2944 | 67.8709 | 70.7788 | 60.8775 | 8304 | 3931 | 8388 | 3463 | 3380 | 97.6032 | |
| gduggal-snapplat | SNP | ti | map_siren | * | 97.1306 | 96.0829 | 98.2013 | 65.7243 | 96424 | 3931 | 96473 | 1767 | 855 | 48.3871 | |
| ciseli-custom | SNP | ti | map_l150_m1_e0 | het | 73.8384 | 68.2296 | 80.4520 | 83.6682 | 8440 | 3930 | 8437 | 2050 | 62 | 3.0244 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 83.1973 | 74.7833 | 93.7446 | 68.3849 | 11649 | 3928 | 61758 | 4121 | 4009 | 97.2822 | |
| ckim-isaac | SNP | ti | map_l150_m2_e1 | homalt | 65.7188 | 48.9666 | 99.8939 | 70.0833 | 3767 | 3926 | 3767 | 4 | 4 | 100.0000 | |
| qzeng-custom | SNP | ti | map_l150_m2_e0 | het | 80.5235 | 69.5753 | 95.5605 | 89.8900 | 8962 | 3919 | 8933 | 415 | 349 | 84.0964 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 69.3783 | 53.2297 | 99.5922 | 52.1673 | 4450 | 3910 | 4396 | 18 | 16 | 88.8889 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 69.3783 | 53.2297 | 99.5922 | 52.1673 | 4450 | 3910 | 4396 | 18 | 16 | 88.8889 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 70.3858 | 62.2960 | 80.8903 | 55.0300 | 6452 | 3905 | 7814 | 1846 | 1272 | 68.9057 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 81.4567 | 75.6715 | 88.1998 | 59.8076 | 12143 | 3904 | 12273 | 1642 | 1435 | 87.3934 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 30.0306 | 17.9045 | 93.0510 | 37.7282 | 851 | 3902 | 857 | 64 | 62 | 96.8750 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 76.6857 | 62.3443 | 99.5964 | 36.2241 | 6457 | 3900 | 6416 | 26 | 21 | 80.7692 | |
| egarrison-hhga | INDEL | D1_5 | HG002compoundhet | * | 69.0217 | 68.1406 | 69.9260 | 60.9500 | 8337 | 3898 | 8410 | 3617 | 3521 | 97.3459 | |
| qzeng-custom | SNP | tv | HG002complexvar | * | 99.0948 | 98.4189 | 99.7800 | 23.2771 | 242263 | 3892 | 238613 | 526 | 243 | 46.1977 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 82.9662 | 72.2705 | 97.3775 | 48.0824 | 10141 | 3891 | 10137 | 273 | 266 | 97.4359 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 79.2963 | 71.7737 | 88.5804 | 40.3166 | 9894 | 3891 | 10720 | 1382 | 1368 | 98.9870 | |
| asubramanian-gatk | SNP | tv | HG002complexvar | homalt | 97.9093 | 95.9142 | 99.9890 | 23.2773 | 91225 | 3886 | 91211 | 10 | 8 | 80.0000 | |
| mlin-fermikit | INDEL | I6_15 | HG002compoundhet | * | 62.8773 | 55.7315 | 72.1249 | 36.3543 | 4891 | 3885 | 4898 | 1893 | 1888 | 99.7359 | |
| ckim-isaac | SNP | ti | map_l150_m2_e0 | homalt | 65.7563 | 49.0021 | 99.9197 | 70.0457 | 3732 | 3884 | 3732 | 3 | 3 | 100.0000 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 53.7099 | 42.3437 | 73.4172 | 63.2026 | 2851 | 3882 | 3850 | 1394 | 367 | 26.3271 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 60.3325 | 43.6538 | 97.6360 | 47.3850 | 3006 | 3880 | 3428 | 83 | 79 | 95.1807 | |
| gduggal-bwaplat | SNP | tv | map_l100_m2_e1 | homalt | 73.6570 | 58.2993 | 100.0000 | 74.6090 | 5423 | 3879 | 5422 | 0 | 0 | ||
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 45.4191 | 32.4145 | 75.8496 | 67.6203 | 1858 | 3874 | 1674 | 533 | 342 | 64.1651 | |
| anovak-vg | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 47.9368 | 36.5290 | 69.7055 | 72.0207 | 2229 | 3873 | 9137 | 3971 | 2851 | 71.7955 | |
| ltrigg-rtg2 | INDEL | * | * | * | 99.2539 | 98.8759 | 99.6347 | 56.1284 | 340668 | 3873 | 340411 | 1248 | 516 | 41.3462 | |
| ciseli-custom | SNP | * | HG002compoundhet | * | 73.2436 | 85.0050 | 64.3413 | 46.5864 | 21950 | 3872 | 21988 | 12186 | 1203 | 9.8720 | |
| anovak-vg | SNP | ti | map_l125_m1_e0 | * | 81.2273 | 86.8110 | 76.3184 | 74.3923 | 25466 | 3869 | 25253 | 7836 | 1746 | 22.2818 | |
| qzeng-custom | SNP | ti | map_l100_m2_e1 | homalt | 88.0999 | 79.0797 | 99.4428 | 59.4081 | 14625 | 3869 | 14457 | 81 | 75 | 92.5926 | |