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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 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
24801-24850 / 86044 show all | |||||||||||||||
hfeng-pmm2 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 91.6667 | 84.6154 | 100.0000 | 42.4110 | 759 | 138 | 793 | 0 | 0 | ||
bgallagher-sentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8224 | 99.6454 | 100.0000 | 42.4180 | 1124 | 4 | 1124 | 0 | 0 | ||
ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.7777 | 96.0123 | 99.6093 | 42.4195 | 9992 | 415 | 9942 | 39 | 16 | 41.0256 | |
ckim-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.8130 | 100.0000 | 99.6267 | 42.4234 | 2138 | 0 | 2135 | 8 | 2 | 25.0000 | |
egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 97.4927 | 96.2865 | 98.7296 | 42.4242 | 1089 | 42 | 1088 | 14 | 12 | 85.7143 | |
eyeh-varpipe | INDEL | D1_5 | tech_badpromoters | * | 89.4737 | 89.4737 | 89.4737 | 42.4242 | 17 | 2 | 17 | 2 | 2 | 100.0000 | |
asubramanian-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.8791 | 98.9123 | 96.8672 | 42.4242 | 4638 | 51 | 4638 | 150 | 2 | 1.3333 | |
astatham-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.7919 | 97.6127 | 100.0000 | 42.4274 | 1104 | 27 | 1110 | 0 | 0 | ||
gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 55.8292 | 50.1922 | 62.8926 | 42.4297 | 6919 | 6866 | 6849 | 4041 | 3720 | 92.0564 | |
egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 78.8405 | 65.4387 | 99.1453 | 42.4354 | 977 | 516 | 928 | 8 | 7 | 87.5000 | |
hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 97.8546 | 96.4789 | 99.2701 | 42.4370 | 137 | 5 | 136 | 1 | 1 | 100.0000 | |
eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 55.8126 | 45.6817 | 71.7174 | 42.4460 | 2888 | 3434 | 6598 | 2602 | 2576 | 99.0008 | |
eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 55.8126 | 45.6817 | 71.7174 | 42.4460 | 2888 | 3434 | 6598 | 2602 | 2576 | 99.0008 | |
jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.4266 | 99.5114 | 95.4273 | 42.4504 | 5092 | 25 | 5092 | 244 | 244 | 100.0000 | |
eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 6.0167 | 3.3981 | 26.2295 | 42.4528 | 7 | 199 | 32 | 90 | 74 | 82.2222 | |
ckim-vqsr | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.8363 | 99.9532 | 99.7196 | 42.4576 | 2137 | 1 | 2134 | 6 | 2 | 33.3333 | |
asubramanian-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.1590 | 93.4295 | 99.0528 | 42.4608 | 2915 | 205 | 3451 | 33 | 31 | 93.9394 | |
gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 98.7659 | 98.1114 | 99.4293 | 42.4615 | 4000 | 77 | 4007 | 23 | 16 | 69.5652 | |
anovak-vg | INDEL | I16_PLUS | HG002complexvar | * | 33.1975 | 24.5225 | 51.3699 | 42.4631 | 321 | 988 | 300 | 284 | 225 | 79.2254 | |
ltrigg-rtg1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 97.7725 | 95.8037 | 99.8239 | 42.4645 | 4452 | 195 | 4535 | 8 | 8 | 100.0000 | |
dgrover-gatk | SNP | ti | tech_badpromoters | homalt | 98.7952 | 100.0000 | 97.6190 | 42.4658 | 41 | 0 | 41 | 1 | 1 | 100.0000 | |
ckim-isaac | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 92.2162 | 86.6135 | 98.5938 | 42.4667 | 3151 | 487 | 3155 | 45 | 26 | 57.7778 | |
ckim-dragen | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.7237 | 99.8934 | 99.5546 | 42.4719 | 4684 | 5 | 4694 | 21 | 2 | 9.5238 | |
gduggal-snapfb | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 42.8116 | 28.1132 | 89.7196 | 42.4731 | 149 | 381 | 96 | 11 | 10 | 90.9091 | |
hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.9247 | 98.1508 | 99.7110 | 42.4771 | 690 | 13 | 690 | 2 | 1 | 50.0000 | |
ckim-dragen | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.7395 | 97.7629 | 99.7358 | 42.4788 | 2622 | 60 | 2643 | 7 | 7 | 100.0000 | |
astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.7781 | 99.6454 | 99.9111 | 42.4847 | 1124 | 4 | 1124 | 1 | 1 | 100.0000 | |
gduggal-snapvard | INDEL | I6_15 | * | het | 64.9859 | 82.1571 | 53.7516 | 42.4853 | 8242 | 1790 | 11591 | 9973 | 7974 | 79.9559 | |
hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.6832 | 96.0089 | 99.4168 | 42.4933 | 19774 | 822 | 19775 | 116 | 110 | 94.8276 | |
jli-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 91.3043 | 84.0000 | 100.0000 | 42.5000 | 21 | 4 | 23 | 0 | 0 | ||
ckim-isaac | INDEL | * | func_cds | het | 97.8678 | 96.7290 | 99.0338 | 42.5000 | 207 | 7 | 205 | 2 | 1 | 50.0000 | |
ndellapenna-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 89.6217 | 88.0000 | 91.3043 | 42.5000 | 22 | 3 | 21 | 2 | 0 | 0.0000 | |
anovak-vg | INDEL | D1_5 | func_cds | het | 90.3955 | 94.1176 | 86.9565 | 42.5000 | 80 | 5 | 80 | 12 | 8 | 66.6667 | |
gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 98.6524 | 97.4079 | 99.9291 | 42.5020 | 1428 | 38 | 1410 | 1 | 0 | 0.0000 | |
ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.0126 | 98.2938 | 99.7419 | 42.5046 | 3111 | 54 | 3091 | 8 | 8 | 100.0000 | |
anovak-vg | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 23.1772 | 16.4208 | 39.3809 | 42.5111 | 345 | 1756 | 458 | 705 | 585 | 82.9787 | |
jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 42.1139 | 37.4782 | 48.0583 | 42.5126 | 7719 | 12877 | 7710 | 8333 | 8271 | 99.2560 | |
gduggal-bwaplat | SNP | tv | func_cds | * | 99.4027 | 98.9934 | 99.8155 | 42.5143 | 4327 | 44 | 4327 | 8 | 0 | 0.0000 | |
ltrigg-rtg1 | SNP | * | HG002compoundhet | het | 98.6093 | 97.5384 | 99.7040 | 42.5144 | 13829 | 349 | 13809 | 41 | 9 | 21.9512 | |
hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.9986 | 98.4353 | 99.5683 | 42.5145 | 692 | 11 | 692 | 3 | 2 | 66.6667 | |
gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 80.8243 | 69.1149 | 97.3105 | 42.5158 | 1882 | 841 | 796 | 22 | 22 | 100.0000 | |
hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 84.8790 | 77.9848 | 93.1104 | 42.5160 | 921 | 260 | 919 | 68 | 68 | 100.0000 | |
raldana-dualsentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.9441 | 95.7602 | 98.1576 | 42.5181 | 9057 | 401 | 9057 | 170 | 166 | 97.6471 | |
dgrover-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.8372 | 97.7011 | 100.0000 | 42.5246 | 1105 | 26 | 1111 | 0 | 0 | ||
hfeng-pmm3 | SNP | tv | HG002compoundhet | homalt | 99.8376 | 99.8229 | 99.8524 | 42.5250 | 3382 | 6 | 3382 | 5 | 5 | 100.0000 | |
jpowers-varprowl | INDEL | I6_15 | * | homalt | 79.1239 | 68.4565 | 93.7294 | 42.5350 | 4271 | 1968 | 4275 | 286 | 264 | 92.3077 | |
gduggal-snapvard | INDEL | D6_15 | HG002complexvar | homalt | 48.4509 | 33.4474 | 87.8641 | 42.5384 | 391 | 778 | 362 | 50 | 46 | 92.0000 | |
anovak-vg | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 61.6176 | 70.8333 | 54.5238 | 42.5445 | 153 | 63 | 229 | 191 | 166 | 86.9110 | |
mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 94.6117 | 94.0740 | 95.1557 | 42.5447 | 6334 | 399 | 6325 | 322 | 313 | 97.2050 | |
qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 97.5207 | 98.4691 | 96.5904 | 42.5528 | 3602 | 56 | 6799 | 240 | 41 | 17.0833 |