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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
70301-70350 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | I16_PLUS | HG002compoundhet | * | 94.8024 | 92.3472 | 97.3917 | 52.6892 | 1979 | 164 | 1979 | 53 | 52 | 98.1132 | |
| anovak-vg | SNP | * | map_l250_m2_e1 | homalt | 84.0320 | 72.8109 | 99.3418 | 88.4510 | 1979 | 739 | 1962 | 13 | 9 | 69.2308 | |
| astatham-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.7032 | 97.7767 | 99.6475 | 68.5461 | 1979 | 45 | 1979 | 7 | 5 | 71.4286 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.9066 | 93.0451 | 96.8442 | 70.4071 | 1980 | 148 | 1964 | 64 | 54 | 84.3750 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 78.4458 | 66.0000 | 96.6764 | 83.1355 | 1980 | 1020 | 1978 | 68 | 17 | 25.0000 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.4502 | 93.0451 | 95.8984 | 70.3618 | 1980 | 148 | 1964 | 84 | 78 | 92.8571 | |
| ckim-gatk | SNP | * | map_l150_m0_e0 | homalt | 65.2389 | 48.4226 | 99.9495 | 85.6968 | 1980 | 2109 | 1980 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.6320 | 97.9249 | 99.3493 | 69.0808 | 1982 | 42 | 1985 | 13 | 5 | 38.4615 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.5787 | 91.0009 | 94.2122 | 75.0968 | 1982 | 196 | 1758 | 108 | 96 | 88.8889 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 77.3064 | 63.5256 | 98.7224 | 46.6579 | 1982 | 1138 | 2009 | 26 | 26 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 94.1085 | 91.0009 | 97.4359 | 68.1633 | 1982 | 196 | 1976 | 52 | 27 | 51.9231 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 50.1828 | 34.9234 | 89.1245 | 58.3302 | 1984 | 3697 | 1975 | 241 | 212 | 87.9668 | |
| asubramanian-gatk | INDEL | * | map_l100_m2_e1 | het | 89.6239 | 84.6778 | 95.1836 | 90.0945 | 1984 | 359 | 1996 | 101 | 13 | 12.8713 | |
| hfeng-pmm3 | INDEL | I16_PLUS | HG002compoundhet | * | 95.0875 | 92.5805 | 97.7340 | 52.1790 | 1984 | 159 | 1984 | 46 | 45 | 97.8261 | |
| cchapple-custom | INDEL | I16_PLUS | HG002compoundhet | * | 94.6047 | 92.5805 | 96.7194 | 51.6153 | 1984 | 159 | 2506 | 85 | 81 | 95.2941 | |
| ckim-dragen | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.6398 | 98.0237 | 99.2636 | 68.7768 | 1984 | 40 | 2022 | 15 | 3 | 20.0000 | |
| ghariani-varprowl | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 90.5692 | 98.0237 | 84.1684 | 80.1687 | 1984 | 40 | 1999 | 376 | 4 | 1.0638 | |
| gduggal-snapplat | INDEL | * | map_siren | homalt | 83.6919 | 74.7269 | 95.1011 | 85.8909 | 1984 | 671 | 2116 | 109 | 16 | 14.6789 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 50.1080 | 34.9234 | 88.6547 | 58.7648 | 1984 | 3697 | 1977 | 253 | 213 | 84.1897 | |
| egarrison-hhga | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.3636 | 98.0237 | 98.7058 | 69.2437 | 1984 | 40 | 1983 | 26 | 6 | 23.0769 | |
| jpowers-varprowl | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.9859 | 98.1225 | 95.8753 | 79.7750 | 1986 | 38 | 1999 | 86 | 3 | 3.4884 | |
| gduggal-bwaplat | SNP | ti | map_l250_m2_e1 | * | 56.1811 | 39.1253 | 99.5990 | 97.1464 | 1986 | 3090 | 1987 | 8 | 2 | 25.0000 | |
| astatham-gatk | INDEL | I16_PLUS | HG002compoundhet | * | 94.5316 | 92.7671 | 96.3645 | 52.8349 | 1988 | 155 | 1988 | 75 | 75 | 100.0000 | |
| anovak-vg | INDEL | I6_15 | HG002complexvar | * | 48.0486 | 41.4858 | 57.0779 | 45.2877 | 1988 | 2804 | 2008 | 1510 | 1270 | 84.1060 | |
| hfeng-pmm1 | INDEL | I16_PLUS | HG002compoundhet | * | 95.0514 | 92.7671 | 97.4510 | 52.1351 | 1988 | 155 | 1988 | 52 | 50 | 96.1538 | |
| ghariani-varprowl | INDEL | * | map_l125_m1_e0 | * | 91.7859 | 94.3996 | 89.3130 | 93.6193 | 1989 | 118 | 1989 | 238 | 77 | 32.3529 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 85.7747 | 91.3682 | 80.8266 | 73.3477 | 1990 | 188 | 1897 | 450 | 430 | 95.5556 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.0947 | 93.5620 | 94.6334 | 73.4309 | 1991 | 137 | 1975 | 112 | 96 | 85.7143 | |
| jmaeng-gatk | SNP | * | map_l150_m0_e0 | homalt | 65.4719 | 48.6916 | 99.8996 | 84.7432 | 1991 | 2098 | 1991 | 2 | 2 | 100.0000 | |
| jpowers-varprowl | SNP | * | map_l250_m0_e0 | * | 92.2045 | 93.3489 | 91.0878 | 95.0147 | 1993 | 142 | 1993 | 195 | 31 | 15.8974 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.3775 | 98.4684 | 96.3105 | 71.9263 | 1993 | 31 | 2010 | 77 | 2 | 2.5974 | |
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 96.3741 | 93.2180 | 99.7514 | 32.0838 | 1993 | 145 | 2006 | 5 | 0 | 0.0000 | |
| gduggal-snapfb | SNP | * | map_l250_m0_e0 | * | 93.7882 | 93.3489 | 94.2317 | 93.9033 | 1993 | 142 | 1993 | 122 | 43 | 35.2459 | |
| gduggal-snapvard | SNP | * | map_l250_m0_e0 | * | 79.3745 | 93.3489 | 69.0393 | 94.3087 | 1993 | 142 | 1969 | 883 | 24 | 2.7180 | |
| gduggal-snapfb | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 57.6740 | 98.5178 | 40.7711 | 77.3433 | 1994 | 30 | 2041 | 2965 | 42 | 1.4165 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 39.8947 | 28.8609 | 64.5870 | 56.5465 | 1994 | 4915 | 1822 | 999 | 788 | 78.8789 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 93.4024 | 92.4861 | 94.3370 | 90.4803 | 1994 | 162 | 1999 | 120 | 81 | 67.5000 | |
| dgrover-gatk | INDEL | I16_PLUS | HG002compoundhet | * | 94.7743 | 93.0938 | 96.5167 | 53.0120 | 1995 | 148 | 1995 | 72 | 72 | 100.0000 | |
| ciseli-custom | INDEL | D16_PLUS | * | het | 73.2078 | 63.1529 | 87.0708 | 54.9379 | 1995 | 1164 | 2054 | 305 | 262 | 85.9016 | |
| qzeng-custom | SNP | tv | map_l150_m0_e0 | het | 79.7044 | 70.2075 | 92.1723 | 93.6869 | 1996 | 847 | 1990 | 169 | 138 | 81.6568 | |
| jmaeng-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 99.0330 | 98.6660 | 99.4027 | 68.8043 | 1997 | 27 | 1997 | 12 | 2 | 16.6667 | |
| rpoplin-dv42 | INDEL | D16_PLUS | HG002compoundhet | * | 86.6377 | 85.3054 | 88.0123 | 33.8869 | 1997 | 344 | 1997 | 272 | 272 | 100.0000 | |
| gduggal-bwafb | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.7638 | 98.6660 | 89.3256 | 80.9138 | 1997 | 27 | 2000 | 239 | 13 | 5.4393 | |
| jli-custom | INDEL | I16_PLUS | HG002compoundhet | * | 95.4155 | 93.2338 | 97.7017 | 49.8529 | 1998 | 145 | 1998 | 47 | 42 | 89.3617 | |
| ckim-vqsr | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.9599 | 98.7154 | 99.2056 | 68.9820 | 1998 | 26 | 1998 | 16 | 7 | 43.7500 | |
| anovak-vg | INDEL | I6_15 | HG002compoundhet | * | 31.2822 | 22.7666 | 49.9744 | 31.5356 | 1998 | 6778 | 1954 | 1956 | 1488 | 76.0736 | |
| asubramanian-gatk | SNP | tv | map_l150_m2_e1 | het | 42.7242 | 27.1911 | 99.6507 | 95.4527 | 1998 | 5350 | 1997 | 7 | 1 | 14.2857 | |
| eyeh-varpipe | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.4797 | 98.7648 | 86.9467 | 79.4810 | 1999 | 25 | 1925 | 289 | 9 | 3.1142 | |
| ckim-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.9370 | 98.8636 | 99.0104 | 68.9077 | 2001 | 23 | 2001 | 20 | 7 | 35.0000 | |
| dgrover-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.9859 | 98.8636 | 99.1085 | 68.8570 | 2001 | 23 | 2001 | 18 | 6 | 33.3333 | |