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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 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
63751-63800 / 86044 show all | |||||||||||||||
ltrigg-rtg1 | INDEL | I6_15 | HG002compoundhet | * | 94.7100 | 90.6791 | 99.1159 | 32.9210 | 7958 | 818 | 7848 | 70 | 64 | 91.4286 | |
cchapple-custom | INDEL | D1_5 | func_cds | * | 99.6885 | 100.0000 | 99.3789 | 32.9167 | 159 | 0 | 160 | 1 | 0 | 0.0000 | |
ltrigg-rtg1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.7034 | 94.0086 | 99.5573 | 32.9140 | 7610 | 485 | 7646 | 34 | 34 | 100.0000 | |
egarrison-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 74.6483 | 60.2410 | 98.1132 | 32.9114 | 50 | 33 | 52 | 1 | 1 | 100.0000 | |
cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.8138 | 96.2869 | 99.3900 | 32.9111 | 6431 | 248 | 13686 | 84 | 81 | 96.4286 | |
asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.3023 | 95.7627 | 98.8922 | 32.9054 | 904 | 40 | 982 | 11 | 10 | 90.9091 | |
ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.0099 | 98.0392 | 100.0000 | 32.8947 | 50 | 1 | 51 | 0 | 0 | ||
ltrigg-rtg2 | SNP | * | HG002compoundhet | homalt | 99.4265 | 98.9241 | 99.9340 | 32.8863 | 10666 | 116 | 10603 | 7 | 6 | 85.7143 | |
rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 94.9496 | 91.0460 | 99.2028 | 32.8775 | 1088 | 107 | 1120 | 9 | 9 | 100.0000 | |
ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.0913 | 94.4749 | 99.8568 | 32.8741 | 2069 | 121 | 2092 | 3 | 3 | 100.0000 | |
hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.0416 | 94.2633 | 99.9886 | 32.8733 | 8758 | 533 | 8802 | 1 | 0 | 0.0000 | |
hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.0416 | 94.2633 | 99.9886 | 32.8733 | 8758 | 533 | 8802 | 1 | 0 | 0.0000 | |
ckim-dragen | INDEL | D6_15 | * | hetalt | 96.4645 | 93.5894 | 99.5217 | 32.8589 | 7650 | 524 | 7699 | 37 | 37 | 100.0000 | |
asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.2978 | 94.0048 | 98.7055 | 32.8581 | 9847 | 628 | 10599 | 139 | 132 | 94.9640 | |
ckim-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.7528 | 96.0459 | 99.5215 | 32.8514 | 753 | 31 | 832 | 4 | 4 | 100.0000 | |
ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.7528 | 96.0459 | 99.5215 | 32.8514 | 753 | 31 | 832 | 4 | 4 | 100.0000 | |
jli-custom | INDEL | I1_5 | func_cds | * | 100.0000 | 100.0000 | 100.0000 | 32.8358 | 180 | 0 | 180 | 0 | 0 | ||
ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 98.4378 | 97.3195 | 99.5821 | 32.8253 | 6644 | 183 | 6672 | 28 | 28 | 100.0000 | |
raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 94.9982 | 90.5081 | 99.9572 | 32.8251 | 2298 | 241 | 2334 | 1 | 1 | 100.0000 | |
gduggal-bwafb | INDEL | * | func_cds | homalt | 97.9684 | 96.0177 | 100.0000 | 32.8173 | 217 | 9 | 217 | 0 | 0 | ||
ndellapenna-hhga | INDEL | D16_PLUS | HG002compoundhet | hetalt | 63.9739 | 47.1473 | 99.4764 | 32.8056 | 909 | 1019 | 760 | 4 | 3 | 75.0000 | |
hfeng-pmm1 | INDEL | D6_15 | HG002compoundhet | * | 95.4940 | 92.9354 | 98.1974 | 32.8011 | 8393 | 638 | 8389 | 154 | 150 | 97.4026 | |
ckim-dragen | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.3919 | 95.3611 | 99.5111 | 32.7822 | 6496 | 316 | 6513 | 32 | 32 | 100.0000 | |
eyeh-varpipe | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.8435 | 99.7712 | 99.9160 | 32.7499 | 1308 | 3 | 1190 | 1 | 1 | 100.0000 | |
jli-custom | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.7622 | 99.8232 | 99.7013 | 32.7459 | 7342 | 13 | 7343 | 22 | 3 | 13.6364 | |
astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 99.1576 | 98.5265 | 99.7969 | 32.7413 | 1471 | 22 | 1474 | 3 | 3 | 100.0000 | |
jmaeng-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.5532 | 95.6633 | 99.5192 | 32.7405 | 750 | 34 | 828 | 4 | 4 | 100.0000 | |
qzeng-custom | INDEL | D16_PLUS | HG002compoundhet | * | 75.9486 | 81.4609 | 71.1351 | 32.7367 | 1907 | 434 | 2112 | 857 | 326 | 38.0397 | |
bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.9298 | 94.4344 | 99.5608 | 32.7290 | 9892 | 583 | 9974 | 44 | 44 | 100.0000 | |
dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.1571 | 94.8660 | 99.5615 | 32.7282 | 8814 | 477 | 8855 | 39 | 37 | 94.8718 | |
dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.1571 | 94.8660 | 99.5615 | 32.7282 | 8814 | 477 | 8855 | 39 | 37 | 94.8718 | |
ckim-vqsr | INDEL | D1_5 | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 32.7273 | 74 | 0 | 74 | 0 | 0 | ||
rpoplin-dv42 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 60.0000 | 43.3735 | 97.2973 | 32.7273 | 36 | 47 | 36 | 1 | 1 | 100.0000 | |
ckim-gatk | INDEL | D1_5 | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 32.7273 | 74 | 0 | 74 | 0 | 0 | ||
gduggal-bwavard | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.6866 | 97.5389 | 99.8617 | 32.7198 | 6579 | 166 | 6497 | 9 | 7 | 77.7778 | |
ckim-isaac | INDEL | * | HG002compoundhet | hetalt | 88.0188 | 79.0747 | 99.2444 | 32.7152 | 19911 | 5269 | 20095 | 153 | 126 | 82.3529 | |
bgallagher-sentieon | INDEL | D6_15 | * | hetalt | 96.5632 | 93.7974 | 99.4971 | 32.7057 | 7667 | 507 | 7716 | 39 | 38 | 97.4359 | |
mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 78.2556 | 64.3957 | 99.7182 | 32.7011 | 5983 | 3308 | 6015 | 17 | 17 | 100.0000 | |
mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 78.2556 | 64.3957 | 99.7182 | 32.7011 | 5983 | 3308 | 6015 | 17 | 17 | 100.0000 | |
asubramanian-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.2194 | 86.3886 | 98.8943 | 32.6995 | 1574 | 248 | 1610 | 18 | 16 | 88.8889 | |
jlack-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 88.0509 | 79.0340 | 99.3902 | 32.6949 | 1440 | 382 | 1467 | 9 | 8 | 88.8889 | |
hfeng-pmm3 | INDEL | D6_15 | HG002compoundhet | * | 95.1894 | 92.4704 | 98.0731 | 32.6928 | 8351 | 680 | 8347 | 164 | 158 | 96.3415 | |
gduggal-bwavard | INDEL | I1_5 | HG002complexvar | homalt | 96.0632 | 92.4747 | 99.9414 | 32.6716 | 12436 | 1012 | 11931 | 7 | 5 | 71.4286 | |
cchapple-custom | SNP | tv | func_cds | * | 99.5556 | 99.9085 | 99.2053 | 32.6708 | 4367 | 4 | 4369 | 35 | 0 | 0.0000 | |
ltrigg-rtg2 | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.7995 | 99.6294 | 99.9702 | 32.6604 | 6720 | 25 | 6703 | 2 | 1 | 50.0000 | |
raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.7169 | 95.5357 | 100.0000 | 32.6547 | 749 | 35 | 827 | 0 | 0 | ||
hfeng-pmm1 | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.9452 | 99.9270 | 99.9635 | 32.6526 | 2736 | 2 | 2736 | 1 | 1 | 100.0000 | |
eyeh-varpipe | INDEL | D6_15 | HG002compoundhet | * | 39.7758 | 35.3560 | 45.4585 | 32.6471 | 3193 | 5838 | 3138 | 3765 | 3754 | 99.7078 | |
hfeng-pmm2 | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.1378 | 87.1570 | 100.0000 | 32.6259 | 1588 | 234 | 1619 | 0 | 0 | ||
dgrover-gatk | SNP | tv | func_cds | het | 99.8496 | 99.9624 | 99.7370 | 32.6247 | 2656 | 1 | 2655 | 7 | 0 | 0.0000 |