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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
15751-15800 / 86044 show all | |||||||||||||||
| ltrigg-rtg2 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.4995 | 97.5791 | 95.4436 | 69.9221 | 1975 | 49 | 1990 | 95 | 2 | 2.1053 | |
| ndellapenna-hhga | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.9401 | 97.5296 | 98.3541 | 69.0300 | 1974 | 50 | 1972 | 33 | 5 | 15.1515 | |
| ckim-vqsr | INDEL | I16_PLUS | HG002compoundhet | * | 94.1794 | 92.1139 | 96.3397 | 52.0365 | 1974 | 169 | 1974 | 75 | 75 | 100.0000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.4568 | 90.6336 | 94.3548 | 75.3152 | 1974 | 204 | 1755 | 105 | 95 | 90.4762 | |
| ckim-gatk | SNP | ti | map_l250_m2_e0 | het | 74.5328 | 60.6638 | 96.6226 | 96.6749 | 1974 | 1280 | 1974 | 69 | 9 | 13.0435 | |
| ciseli-custom | SNP | ti | map_l250_m2_e1 | het | 64.3765 | 59.8060 | 69.7034 | 93.5598 | 1973 | 1326 | 1974 | 858 | 20 | 2.3310 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 93.3712 | 87.5666 | 100.0000 | 59.6774 | 1972 | 280 | 1975 | 0 | 0 | ||
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.5176 | 92.5752 | 96.5432 | 70.8171 | 1970 | 158 | 1955 | 70 | 56 | 80.0000 | |
| hfeng-pmm3 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.3762 | 97.2826 | 99.4947 | 68.4722 | 1969 | 55 | 1969 | 10 | 0 | 0.0000 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 91.0894 | 90.4040 | 91.7852 | 74.4242 | 1969 | 209 | 1743 | 156 | 147 | 94.2308 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 92.1665 | 91.3265 | 93.0222 | 72.9912 | 1969 | 187 | 1973 | 148 | 100 | 67.5676 | |
| jmaeng-gatk | SNP | ti | map_l250_m2_e0 | het | 74.4705 | 60.5101 | 96.8043 | 96.7872 | 1969 | 1285 | 1969 | 65 | 8 | 12.3077 | |
| ltrigg-rtg1 | SNP | * | map_l250_m0_e0 | * | 95.7430 | 92.1780 | 99.5949 | 87.5418 | 1968 | 167 | 1967 | 8 | 3 | 37.5000 | |
| jmaeng-gatk | INDEL | I16_PLUS | HG002compoundhet | * | 94.0923 | 91.7872 | 96.5162 | 52.1372 | 1967 | 176 | 1967 | 71 | 70 | 98.5915 | |
| gduggal-snapfb | INDEL | * | map_l125_m1_e0 | * | 94.2593 | 93.3555 | 95.1807 | 86.4184 | 1967 | 140 | 1975 | 100 | 24 | 24.0000 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 0.0000 | 24.4075 | 0.0000 | 0.0000 | 1967 | 6092 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 0.0000 | 24.4075 | 0.0000 | 0.0000 | 1967 | 6092 | 0 | 0 | 0 | ||
| qzeng-custom | SNP | tv | map_l250_m2_e1 | * | 78.0956 | 67.4211 | 92.7860 | 95.3708 | 1966 | 950 | 1955 | 152 | 125 | 82.2368 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 79.2669 | 90.1745 | 70.7134 | 62.8847 | 1964 | 214 | 2260 | 936 | 894 | 95.5128 | |
| raldana-dualsentieon | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.1509 | 97.0356 | 99.2922 | 64.9042 | 1964 | 60 | 1964 | 14 | 0 | 0.0000 | |
| gduggal-bwaplat | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 67.4105 | 51.3337 | 98.1491 | 56.8902 | 1963 | 1861 | 1962 | 37 | 36 | 97.2973 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.9210 | 92.2462 | 93.6058 | 72.7642 | 1963 | 165 | 1947 | 133 | 117 | 87.9699 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 66.9020 | 71.8258 | 62.6099 | 52.3713 | 1963 | 770 | 2207 | 1318 | 760 | 57.6631 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 92.5093 | 87.1670 | 98.5493 | 64.5442 | 1963 | 289 | 1970 | 29 | 7 | 24.1379 | |
| hfeng-pmm1 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.2228 | 96.9368 | 99.5434 | 64.5886 | 1962 | 62 | 1962 | 9 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 82.5111 | 88.7732 | 77.0743 | 58.5831 | 1961 | 248 | 1960 | 583 | 573 | 98.2847 | |
| hfeng-pmm2 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.0002 | 96.8379 | 99.1907 | 64.6712 | 1960 | 64 | 1961 | 16 | 0 | 0.0000 | |
| gduggal-snapfb | INDEL | D6_15 | HG002complexvar | het | 75.2635 | 62.8205 | 93.8532 | 43.4007 | 1960 | 1160 | 2443 | 160 | 143 | 89.3750 | |
| asubramanian-gatk | SNP | tv | map_l150_m2_e0 | het | 42.5209 | 27.0270 | 99.6439 | 95.4728 | 1960 | 5292 | 1959 | 7 | 1 | 14.2857 | |
| anovak-vg | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 32.9741 | 0.0000 | 0.0000 | 1958 | 3980 | 0 | 0 | 0 | ||
| jli-custom | INDEL | I16_PLUS | * | hetalt | 96.3839 | 93.3270 | 99.6479 | 53.7674 | 1958 | 140 | 1981 | 7 | 7 | 100.0000 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 77.5015 | 89.8990 | 68.1090 | 63.2249 | 1958 | 220 | 2125 | 995 | 950 | 95.4774 | |
| ckim-dragen | INDEL | I16_PLUS | HG002compoundhet | * | 93.5490 | 91.3672 | 95.8374 | 52.5778 | 1958 | 185 | 1957 | 85 | 85 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | map_l250_m2_e0 | * | 56.1308 | 39.0775 | 99.5931 | 97.1311 | 1957 | 3051 | 1958 | 8 | 2 | 25.0000 | |
| eyeh-varpipe | SNP | tv | map_l250_m2_e1 | het | 98.2749 | 99.5420 | 97.0396 | 91.1568 | 1956 | 9 | 1934 | 59 | 4 | 6.7797 | |
| jli-custom | INDEL | I16_PLUS | HG002compoundhet | hetalt | 96.5418 | 93.3588 | 99.9494 | 44.0544 | 1954 | 139 | 1975 | 1 | 1 | 100.0000 | |
| anovak-vg | SNP | * | map_l250_m2_e0 | homalt | 83.9868 | 72.7476 | 99.3333 | 88.4225 | 1954 | 732 | 1937 | 13 | 9 | 69.2308 | |
| asubramanian-gatk | INDEL | * | map_l100_m2_e0 | het | 89.6413 | 84.6987 | 95.1965 | 90.0770 | 1954 | 353 | 1962 | 99 | 13 | 13.1313 | |
| jpowers-varprowl | INDEL | I6_15 | HG002complexvar | het | 76.9804 | 82.9299 | 71.8274 | 56.3262 | 1953 | 402 | 1981 | 777 | 772 | 99.3565 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3623 | 99.9488 | 96.8254 | 41.7173 | 1952 | 1 | 1952 | 64 | 62 | 96.8750 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.2138 | 99.9488 | 96.5381 | 40.8253 | 1952 | 1 | 1952 | 70 | 69 | 98.5714 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.6232 | 99.8976 | 95.4501 | 41.3150 | 1951 | 2 | 1951 | 93 | 92 | 98.9247 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3863 | 99.8976 | 96.9200 | 41.4826 | 1951 | 2 | 1951 | 62 | 62 | 100.0000 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3615 | 99.8976 | 96.8719 | 41.6063 | 1951 | 2 | 1951 | 63 | 62 | 98.4127 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 86.1765 | 80.9208 | 92.1623 | 55.9146 | 1951 | 460 | 1999 | 170 | 145 | 85.2941 | |
| dgrover-gatk | INDEL | I16_PLUS | * | hetalt | 96.2521 | 92.9933 | 99.7475 | 58.1926 | 1951 | 147 | 1975 | 5 | 5 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3615 | 99.8976 | 96.8719 | 41.6063 | 1951 | 2 | 1951 | 63 | 62 | 98.4127 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3863 | 99.8976 | 96.9200 | 41.5335 | 1951 | 2 | 1951 | 62 | 62 | 100.0000 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.1609 | 99.8464 | 98.4848 | 39.5973 | 1950 | 3 | 1950 | 30 | 30 | 100.0000 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 86.6360 | 76.8019 | 99.3583 | 29.3091 | 1950 | 589 | 2013 | 13 | 11 | 84.6154 | |