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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
36801-36850 / 86044 show all | |||||||||||||||
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 77.2126 | 92.3546 | 66.3363 | 73.7008 | 2271 | 188 | 2276 | 1155 | 1093 | 94.6320 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 46.2359 | 35.4839 | 66.3366 | 79.0456 | 66 | 120 | 67 | 34 | 34 | 100.0000 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 60.3133 | 55.2921 | 66.3376 | 42.9617 | 653 | 528 | 672 | 341 | 312 | 91.4956 | |
| astatham-gatk | INDEL | D1_5 | HG002compoundhet | homalt | 79.6703 | 99.6564 | 66.3616 | 87.7109 | 290 | 1 | 290 | 147 | 146 | 99.3197 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 63.5445 | 60.9484 | 66.3717 | 63.9745 | 437 | 280 | 450 | 228 | 159 | 69.7368 | |
| anovak-vg | SNP | ti | map_l150_m0_e0 | het | 74.8246 | 85.7367 | 66.3765 | 86.9328 | 4370 | 727 | 4347 | 2202 | 593 | 26.9301 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 73.2802 | 81.7861 | 66.3768 | 81.5483 | 696 | 155 | 916 | 464 | 182 | 39.2241 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 75.4245 | 87.3154 | 66.3840 | 63.3729 | 7331 | 1065 | 7751 | 3925 | 1802 | 45.9108 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 73.1635 | 81.4815 | 66.3866 | 60.7261 | 88 | 20 | 158 | 80 | 21 | 26.2500 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 57.1106 | 50.0879 | 66.4235 | 43.0727 | 2563 | 2554 | 2732 | 1381 | 1057 | 76.5387 | |
| gduggal-snapfb | SNP | * | * | hetalt | 79.7614 | 99.7704 | 66.4373 | 62.1965 | 869 | 2 | 869 | 439 | 29 | 6.6059 | |
| gduggal-snapfb | SNP | tv | * | hetalt | 79.7614 | 99.7704 | 66.4373 | 62.1965 | 869 | 2 | 869 | 439 | 29 | 6.6059 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 68.5238 | 70.7333 | 66.4482 | 68.8856 | 2122 | 878 | 2230 | 1126 | 242 | 21.4920 | |
| eyeh-varpipe | INDEL | I1_5 | HG002compoundhet | het | 74.0633 | 83.6471 | 66.4499 | 67.5390 | 711 | 139 | 511 | 258 | 225 | 87.2093 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 62.9012 | 59.7110 | 66.4516 | 34.9559 | 1033 | 697 | 1030 | 520 | 432 | 83.0769 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 69.6175 | 73.0888 | 66.4609 | 58.6501 | 2849 | 1049 | 4092 | 2065 | 1377 | 66.6828 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 78.8022 | 96.7658 | 66.4639 | 76.6264 | 748 | 25 | 874 | 441 | 259 | 58.7302 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 75.2916 | 86.8093 | 66.4721 | 57.3739 | 6410 | 974 | 6834 | 3447 | 1755 | 50.9138 | |
| ciseli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 78.7997 | 96.7251 | 66.4796 | 66.7555 | 827 | 28 | 829 | 418 | 3 | 0.7177 | |
| gduggal-bwavard | INDEL | D1_5 | map_l250_m2_e0 | het | 79.3333 | 98.3471 | 66.4804 | 96.1331 | 119 | 2 | 119 | 60 | 4 | 6.6667 | |
| ciseli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 78.3548 | 95.3881 | 66.4830 | 78.8960 | 13899 | 672 | 13998 | 7057 | 339 | 4.8037 | |
| ciseli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 78.3548 | 95.3881 | 66.4830 | 78.8960 | 13899 | 672 | 13998 | 7057 | 339 | 4.8037 | |
| anovak-vg | SNP | tv | map_l125_m1_e0 | het | 77.0260 | 91.5169 | 66.4968 | 76.6933 | 9267 | 859 | 9265 | 4668 | 1021 | 21.8723 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 60.5607 | 55.5947 | 66.5009 | 43.6531 | 6161 | 4921 | 6019 | 3032 | 2878 | 94.9208 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 69.5027 | 72.7855 | 66.5031 | 38.8732 | 11471 | 4289 | 21148 | 10652 | 8272 | 77.6568 | |
| jpowers-varprowl | INDEL | I16_PLUS | * | * | 56.3839 | 48.9258 | 66.5246 | 59.4066 | 3120 | 3257 | 3122 | 1571 | 1564 | 99.5544 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 62.9779 | 59.7881 | 66.5273 | 42.2033 | 14672 | 9868 | 14642 | 7367 | 7111 | 96.5250 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 67.4506 | 68.3983 | 66.5289 | 66.7811 | 316 | 146 | 322 | 162 | 105 | 64.8148 | |
| ciseli-custom | INDEL | * | map_l250_m2_e0 | * | 57.9713 | 51.3595 | 66.5370 | 97.5315 | 170 | 161 | 171 | 86 | 44 | 51.1628 | |
| gduggal-snapvard | SNP | tv | map_l250_m0_e0 | * | 78.0985 | 94.5098 | 66.5434 | 94.1611 | 723 | 42 | 720 | 362 | 4 | 1.1050 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 55.3614 | 47.3958 | 66.5455 | 70.9916 | 182 | 202 | 183 | 92 | 89 | 96.7391 | |
| eyeh-varpipe | INDEL | D6_15 | HG002complexvar | homalt | 74.1328 | 83.6612 | 66.5529 | 48.6865 | 978 | 191 | 975 | 490 | 482 | 98.3673 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 77.8072 | 93.6126 | 66.5680 | 74.1046 | 894 | 61 | 900 | 452 | 50 | 11.0619 | |
| ciseli-custom | INDEL | I1_5 | map_l100_m2_e1 | het | 69.5757 | 72.8395 | 66.5919 | 86.3900 | 590 | 220 | 594 | 298 | 258 | 86.5772 | |
| jpowers-varprowl | INDEL | I6_15 | * | * | 57.4140 | 50.4492 | 66.6100 | 47.5997 | 12523 | 12300 | 12542 | 6287 | 6247 | 99.3638 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 75.4208 | 86.9067 | 66.6165 | 52.9703 | 531 | 80 | 443 | 222 | 213 | 95.9459 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 59.1118 | 53.1250 | 66.6194 | 50.7504 | 952 | 840 | 940 | 471 | 467 | 99.1507 | |
| ciseli-custom | INDEL | I1_5 | map_l100_m1_e0 | het | 69.4206 | 72.4582 | 66.6275 | 85.4704 | 563 | 214 | 567 | 284 | 245 | 86.2676 | |
| ciseli-custom | INDEL | I1_5 | map_l100_m2_e0 | het | 69.5601 | 72.7617 | 66.6284 | 86.3856 | 577 | 216 | 581 | 291 | 251 | 86.2543 | |
| ciseli-custom | INDEL | D16_PLUS | map_l125_m0_e0 | homalt | 80.0000 | 100.0000 | 66.6667 | 95.9459 | 2 | 0 | 2 | 1 | 1 | 100.0000 | |
| ciseli-custom | INDEL | D16_PLUS | map_l250_m2_e0 | * | 50.0000 | 40.0000 | 66.6667 | 97.8102 | 2 | 3 | 2 | 1 | 1 | 100.0000 | |
| ciseli-custom | INDEL | D16_PLUS | map_l250_m2_e1 | * | 50.0000 | 40.0000 | 66.6667 | 97.8723 | 2 | 3 | 2 | 1 | 1 | 100.0000 | |
| ciseli-custom | INDEL | D16_PLUS | tech_badpromoters | * | 57.1429 | 50.0000 | 66.6667 | 40.0000 | 2 | 2 | 2 | 1 | 1 | 100.0000 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_gt200bp_gt95identity_merged | homalt | 80.0000 | 100.0000 | 66.6667 | 99.3671 | 2 | 0 | 2 | 1 | 1 | 100.0000 | |
| ciseli-custom | INDEL | D1_5 | tech_badpromoters | * | 70.0000 | 73.6842 | 66.6667 | 41.6667 | 14 | 5 | 14 | 7 | 3 | 42.8571 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_AllRepeats_gt200bp_gt95identity_merged | het | 66.6667 | 66.6667 | 66.6667 | 98.1132 | 2 | 1 | 2 | 1 | 1 | 100.0000 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_gt200bp_gt95identity_merged | het | 80.0000 | 100.0000 | 66.6667 | 98.0263 | 2 | 0 | 2 | 1 | 1 | 100.0000 | |
| ciseli-custom | INDEL | D6_15 | map_l250_m1_e0 | * | 60.6061 | 55.5556 | 66.6667 | 97.9812 | 10 | 8 | 10 | 5 | 0 | 0.0000 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 12.1212 | 6.6667 | 66.6667 | 89.2857 | 1 | 14 | 2 | 1 | 1 | 100.0000 | |
| ciseli-custom | INDEL | I1_5 | map_l125_m1_e0 | * | 58.9106 | 52.7711 | 66.6667 | 88.0351 | 438 | 392 | 436 | 218 | 187 | 85.7798 | |