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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
65001-65050 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | I1_5 | map_l125_m2_e0 | * | 97.6916 | 98.5998 | 96.8000 | 90.6836 | 845 | 12 | 847 | 28 | 3 | 10.7143 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.6471 | 99.4131 | 99.8821 | 84.7756 | 847 | 5 | 847 | 1 | 1 | 100.0000 | |
| mlin-fermikit | INDEL | I1_5 | map_l100_m2_e1 | * | 72.9543 | 60.7168 | 91.3700 | 78.5863 | 847 | 548 | 847 | 80 | 69 | 86.2500 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 86.4854 | 99.1784 | 76.6727 | 86.8957 | 845 | 7 | 848 | 258 | 212 | 82.1705 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 97.7499 | 98.0301 | 97.4713 | 60.6157 | 846 | 17 | 848 | 22 | 7 | 31.8182 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.8797 | 87.6923 | 98.7194 | 39.9301 | 855 | 120 | 848 | 11 | 11 | 100.0000 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.5305 | 99.7647 | 99.2974 | 52.1032 | 848 | 2 | 848 | 6 | 6 | 100.0000 | |
| bgallagher-sentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 99.4721 | 99.6475 | 99.2974 | 88.2757 | 848 | 3 | 848 | 6 | 5 | 83.3333 | |
| bgallagher-sentieon | SNP | tv | map_l250_m1_e0 | homalt | 99.2393 | 99.0654 | 99.4138 | 85.1935 | 848 | 8 | 848 | 5 | 4 | 80.0000 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 86.6541 | 92.2535 | 81.6956 | 79.2980 | 786 | 66 | 848 | 190 | 161 | 84.7368 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 60.8979 | 43.9836 | 98.9498 | 39.8596 | 859 | 1094 | 848 | 9 | 7 | 77.7778 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m2_e0 | * | 98.8330 | 98.7165 | 98.9498 | 87.7955 | 846 | 11 | 848 | 9 | 2 | 22.2222 | |
| egarrison-hhga | SNP | tv | map_l250_m1_e0 | homalt | 99.4138 | 99.0654 | 99.7647 | 86.4065 | 848 | 8 | 848 | 2 | 2 | 100.0000 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.6475 | 99.7647 | 99.5305 | 50.8083 | 848 | 2 | 848 | 4 | 4 | 100.0000 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.8234 | 99.7647 | 99.8822 | 49.2225 | 848 | 2 | 848 | 1 | 1 | 100.0000 | |
| jli-custom | SNP | tv | map_l250_m1_e0 | homalt | 99.2974 | 99.0654 | 99.5305 | 84.1518 | 848 | 8 | 848 | 4 | 4 | 100.0000 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.6475 | 99.7647 | 99.5305 | 49.7048 | 848 | 2 | 848 | 4 | 4 | 100.0000 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 90.5586 | 84.7305 | 97.2477 | 63.2687 | 849 | 153 | 848 | 24 | 21 | 87.5000 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.7647 | 99.7647 | 99.7647 | 48.5783 | 848 | 2 | 848 | 2 | 2 | 100.0000 | |
| jlack-gatk | INDEL | D1_5 | map_l100_m0_e0 | * | 93.4498 | 98.2619 | 89.0871 | 88.3254 | 848 | 15 | 849 | 104 | 6 | 5.7692 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 75.4613 | 91.1765 | 64.3669 | 39.3284 | 775 | 75 | 849 | 470 | 455 | 96.8085 | |
| gduggal-bwafb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 95.6084 | 99.4152 | 92.0824 | 70.5431 | 850 | 5 | 849 | 73 | 4 | 5.4795 | |
| ckim-dragen | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 99.1798 | 99.1774 | 99.1822 | 88.3012 | 844 | 7 | 849 | 7 | 7 | 100.0000 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.7650 | 99.8824 | 99.6479 | 51.2307 | 849 | 1 | 849 | 3 | 3 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | map_l125_m2_e0 | * | 97.7534 | 98.8331 | 96.6970 | 90.4503 | 847 | 10 | 849 | 29 | 3 | 10.3448 | |
| ckim-isaac | INDEL | * | map_l150_m2_e0 | * | 74.8018 | 60.2983 | 98.4919 | 91.3653 | 849 | 559 | 849 | 13 | 5 | 38.4615 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 74.5086 | 80.7087 | 69.1932 | 71.0477 | 615 | 147 | 849 | 378 | 216 | 57.1429 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6510 | 99.4206 | 99.8824 | 57.6060 | 858 | 5 | 849 | 1 | 1 | 100.0000 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.7650 | 99.8824 | 99.6479 | 51.1188 | 849 | 1 | 849 | 3 | 3 | 100.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.6479 | 99.8824 | 99.4145 | 51.1721 | 849 | 1 | 849 | 5 | 5 | 100.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | map_l125_m2_e0 | * | 98.7770 | 98.8331 | 98.7209 | 87.0110 | 847 | 10 | 849 | 11 | 2 | 18.1818 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 70.6464 | 66.6133 | 75.1993 | 63.7444 | 832 | 417 | 849 | 280 | 193 | 68.9286 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 70.6464 | 66.6133 | 75.1993 | 63.7444 | 832 | 417 | 849 | 280 | 193 | 68.9286 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 94.0522 | 92.1444 | 96.0407 | 70.6215 | 868 | 74 | 849 | 35 | 23 | 65.7143 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.8929 | 99.1813 | 98.6063 | 58.3656 | 848 | 7 | 849 | 12 | 3 | 25.0000 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.7650 | 99.8824 | 99.6479 | 51.0626 | 849 | 1 | 849 | 3 | 3 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 97.0472 | 97.6240 | 96.4773 | 83.0378 | 945 | 23 | 849 | 31 | 21 | 67.7419 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.7650 | 99.8824 | 99.6479 | 51.2307 | 849 | 1 | 849 | 3 | 3 | 100.0000 | |
| jli-custom | INDEL | I1_5 | map_l125_m2_e0 | * | 99.1816 | 98.9498 | 99.4145 | 85.5524 | 848 | 9 | 849 | 5 | 2 | 40.0000 | |
| jmaeng-gatk | SNP | ti | map_l250_m2_e1 | homalt | 64.8360 | 47.9684 | 100.0000 | 92.8276 | 850 | 922 | 850 | 0 | 0 | ||
| ckim-dragen | SNP | tv | map_l250_m1_e0 | homalt | 99.1254 | 99.2991 | 98.9523 | 83.2944 | 850 | 6 | 850 | 9 | 7 | 77.7778 | |
| ckim-gatk | INDEL | D1_5 | map_l100_m0_e0 | * | 95.3440 | 98.3778 | 92.4918 | 89.2439 | 849 | 14 | 850 | 69 | 5 | 7.2464 | |
| hfeng-pmm2 | INDEL | I1_5 | map_l125_m2_e0 | * | 98.8360 | 98.9498 | 98.7224 | 87.0837 | 848 | 9 | 850 | 11 | 2 | 18.1818 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 43.5112 | 89.2820 | 28.7648 | 54.7750 | 858 | 103 | 850 | 2105 | 2053 | 97.5297 | |
| gduggal-snapfb | INDEL | D6_15 | * | hetalt | 74.5835 | 65.2679 | 87.0010 | 49.2731 | 5335 | 2839 | 850 | 127 | 126 | 99.2126 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m0_e0 | * | 98.1515 | 98.3778 | 97.9263 | 86.5655 | 849 | 14 | 850 | 18 | 4 | 22.2222 | |
| eyeh-varpipe | INDEL | * | map_l100_m0_e0 | homalt | 96.1789 | 96.8566 | 95.5107 | 86.4425 | 493 | 16 | 851 | 40 | 34 | 85.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | HG002complexvar | het | 98.3872 | 98.7353 | 98.0415 | 69.0000 | 1093 | 14 | 851 | 17 | 10 | 58.8235 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 97.0978 | 97.8306 | 96.3760 | 82.9898 | 947 | 21 | 851 | 32 | 22 | 68.7500 | |
| ckim-gatk | SNP | ti | map_l250_m2_e1 | homalt | 64.8875 | 48.0248 | 100.0000 | 93.2374 | 851 | 921 | 851 | 0 | 0 | ||