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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
38201-38250 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 92.1875 | 85.5072 | 100.0000 | 54.9618 | 59 | 10 | 59 | 0 | 0 | ||
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 81.0909 | 85.5072 | 77.1084 | 86.6129 | 59 | 10 | 64 | 19 | 14 | 73.6842 | |
| anovak-vg | INDEL | D1_5 | map_l125_m0_e0 | het | 80.1955 | 85.5072 | 75.5051 | 90.4922 | 295 | 50 | 299 | 97 | 38 | 39.1753 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.1644 | 85.5030 | 99.9515 | 30.1491 | 2023 | 343 | 2061 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | INDEL | * | map_l150_m1_e0 | * | 89.9819 | 85.5007 | 94.9587 | 97.6598 | 1144 | 194 | 1149 | 61 | 7 | 11.4754 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 85.1218 | 85.4985 | 84.7484 | 72.4437 | 566 | 96 | 539 | 97 | 47 | 48.4536 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 71.5090 | 85.4985 | 61.4537 | 75.3529 | 566 | 96 | 558 | 350 | 286 | 81.7143 | |
| anovak-vg | INDEL | D1_5 | map_l100_m1_e0 | * | 84.4511 | 85.4978 | 83.4298 | 83.8652 | 1580 | 268 | 1586 | 315 | 119 | 37.7778 | |
| anovak-vg | INDEL | D1_5 | map_l125_m2_e1 | * | 83.4613 | 85.4797 | 81.5359 | 87.6226 | 989 | 168 | 998 | 226 | 83 | 36.7257 | |
| asubramanian-gatk | INDEL | D1_5 | map_l150_m1_e0 | het | 88.2318 | 85.4772 | 91.1700 | 92.4108 | 412 | 70 | 413 | 40 | 4 | 10.0000 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 91.6751 | 85.4753 | 98.8445 | 42.9599 | 6132 | 1042 | 941 | 11 | 11 | 100.0000 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 83.6651 | 85.4732 | 81.9319 | 70.4517 | 1165 | 198 | 1179 | 260 | 119 | 45.7692 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 91.8769 | 85.4651 | 99.3289 | 73.0072 | 147 | 25 | 148 | 1 | 0 | 0.0000 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 87.1624 | 85.4630 | 88.9307 | 63.9481 | 1652 | 281 | 1655 | 206 | 205 | 99.5146 | |
| astatham-gatk | SNP | ti | map_l100_m2_e1 | * | 92.0971 | 85.4623 | 99.8489 | 69.7778 | 42291 | 7194 | 42284 | 64 | 36 | 56.2500 | |
| ciseli-custom | INDEL | I1_5 | * | * | 87.1708 | 85.4583 | 88.9534 | 56.1825 | 128754 | 21909 | 128479 | 15955 | 13768 | 86.2927 | |
| gduggal-bwaplat | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 91.9813 | 85.4583 | 99.5823 | 47.6985 | 3338 | 568 | 3338 | 14 | 1 | 7.1429 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.1569 | 85.4545 | 100.0000 | 87.4309 | 94 | 16 | 91 | 0 | 0 | ||
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 15.1782 | 85.4545 | 8.3287 | 79.8084 | 141 | 24 | 151 | 1662 | 21 | 1.2635 | |
| asubramanian-gatk | INDEL | I1_5 | map_l100_m0_e0 | * | 91.0720 | 85.4512 | 97.4843 | 89.1665 | 464 | 79 | 465 | 12 | 1 | 8.3333 | |
| anovak-vg | SNP | * | map_l100_m0_e0 | * | 81.2078 | 85.4511 | 77.3660 | 74.7301 | 28063 | 4778 | 27745 | 8117 | 2172 | 26.7587 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 76.6206 | 85.4508 | 69.4444 | 82.3834 | 417 | 71 | 425 | 187 | 171 | 91.4439 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 67.0699 | 85.4447 | 55.1993 | 68.7686 | 634 | 108 | 637 | 517 | 507 | 98.0658 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 91.7090 | 85.4430 | 98.9667 | 76.0780 | 270 | 46 | 862 | 9 | 9 | 100.0000 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 91.8622 | 85.4308 | 99.3408 | 88.0041 | 1507 | 257 | 1507 | 10 | 4 | 40.0000 | |
| astatham-gatk | SNP | ti | map_l100_m2_e0 | * | 92.0782 | 85.4292 | 99.8496 | 69.7884 | 41827 | 7134 | 41820 | 63 | 36 | 57.1429 | |
| gduggal-snapplat | SNP | tv | map_l150_m2_e0 | homalt | 92.1411 | 85.4274 | 100.0000 | 76.0916 | 3488 | 595 | 3488 | 0 | 0 | ||
| qzeng-custom | INDEL | D1_5 | HG002compoundhet | * | 88.1713 | 85.4271 | 91.0977 | 64.3947 | 10452 | 1783 | 11502 | 1124 | 856 | 76.1566 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 85.6996 | 85.4251 | 85.9760 | 54.8462 | 633 | 108 | 1502 | 245 | 198 | 80.8163 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 87.8389 | 85.4251 | 90.3930 | 78.7175 | 211 | 36 | 207 | 22 | 19 | 86.3636 | |
| asubramanian-gatk | INDEL | I1_5 | map_l125_m0_e0 | het | 89.6323 | 85.4167 | 94.2857 | 93.1800 | 164 | 28 | 165 | 10 | 0 | 0.0000 | |
| cchapple-custom | INDEL | D16_PLUS | map_l100_m2_e0 | het | 83.6445 | 85.4167 | 81.9444 | 92.5620 | 41 | 7 | 59 | 13 | 7 | 53.8462 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 91.1111 | 85.4167 | 97.6190 | 27.2727 | 164 | 28 | 164 | 4 | 4 | 100.0000 | |
| ckim-isaac | INDEL | I1_5 | segdup | hetalt | 92.1348 | 85.4167 | 100.0000 | 94.7165 | 41 | 7 | 41 | 0 | 0 | ||
| gduggal-bwavard | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 54.1148 | 85.3960 | 39.6066 | 69.0608 | 3450 | 590 | 3443 | 5250 | 4800 | 91.4286 | |
| anovak-vg | INDEL | D1_5 | map_l125_m2_e0 | * | 83.4201 | 85.3893 | 81.5397 | 87.6090 | 976 | 167 | 985 | 223 | 82 | 36.7713 | |
| gduggal-snapplat | INDEL | D1_5 | * | homalt | 88.9829 | 85.3881 | 92.8936 | 64.0746 | 41777 | 7149 | 49006 | 3749 | 2039 | 54.3878 | |
| gduggal-snapfb | INDEL | D6_15 | map_siren | homalt | 89.5161 | 85.3846 | 94.0678 | 84.8912 | 111 | 19 | 111 | 7 | 6 | 85.7143 | |
| anovak-vg | SNP | * | map_l100_m2_e1 | homalt | 91.8309 | 85.3756 | 99.3422 | 61.4163 | 23731 | 4065 | 23410 | 155 | 133 | 85.8065 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 53.9976 | 85.3746 | 39.4857 | 56.3279 | 4991 | 855 | 5021 | 7695 | 7654 | 99.4672 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 53.9976 | 85.3746 | 39.4857 | 56.3279 | 4991 | 855 | 5021 | 7695 | 7654 | 99.4672 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 91.1118 | 85.3688 | 97.6832 | 88.4817 | 5683 | 974 | 5692 | 135 | 24 | 17.7778 | |
| gduggal-snapfb | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 56.9106 | 85.3659 | 42.6829 | 94.4180 | 35 | 6 | 35 | 47 | 6 | 12.7660 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 88.2072 | 85.3659 | 91.2442 | 83.3461 | 210 | 36 | 198 | 19 | 8 | 42.1053 | |
| ndellapenna-hhga | SNP | * | map_l100_m1_e0 | hetalt | 90.9091 | 85.3659 | 97.2222 | 77.7778 | 35 | 6 | 35 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | SNP | tv | map_l100_m1_e0 | hetalt | 90.9091 | 85.3659 | 97.2222 | 77.7778 | 35 | 6 | 35 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 81.3953 | 85.3659 | 77.7778 | 82.8244 | 35 | 6 | 35 | 10 | 5 | 50.0000 | |
| ltrigg-rtg1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.1053 | 85.3659 | 100.0000 | 90.6977 | 35 | 6 | 32 | 0 | 0 | ||
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 77.8308 | 85.3621 | 71.5206 | 64.6147 | 554 | 95 | 555 | 221 | 81 | 36.6516 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.1020 | 85.3602 | 100.0000 | 31.3904 | 1102 | 189 | 1130 | 0 | 0 | ||