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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
24601-24650 / 86044 show all | |||||||||||||||
| ckim-gatk | SNP | * | HG002compoundhet | * | 99.3973 | 99.0009 | 99.7970 | 41.7198 | 25564 | 258 | 25561 | 52 | 38 | 73.0769 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 20.0923 | 11.4118 | 83.9506 | 41.7266 | 97 | 753 | 68 | 13 | 13 | 100.0000 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 78.4631 | 67.4647 | 93.7460 | 41.7311 | 3776 | 1821 | 8829 | 589 | 574 | 97.4533 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 58.8731 | 57.9621 | 59.8131 | 41.7312 | 1132 | 821 | 1216 | 817 | 563 | 68.9106 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.0268 | 98.8184 | 99.2361 | 41.7338 | 2258 | 27 | 2728 | 21 | 10 | 47.6190 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 66.3810 | 65.0448 | 67.7731 | 41.7349 | 15962 | 8578 | 15905 | 7563 | 5364 | 70.9242 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 96.4963 | 97.0192 | 95.9791 | 41.7450 | 17641 | 542 | 17783 | 745 | 376 | 50.4698 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7289 | 99.5326 | 99.9260 | 41.7636 | 4046 | 19 | 4052 | 3 | 3 | 100.0000 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.6976 | 99.5818 | 99.8136 | 41.7639 | 2143 | 9 | 2142 | 4 | 4 | 100.0000 | |
| anovak-vg | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 81.2064 | 88.9071 | 74.7333 | 41.7707 | 5971 | 745 | 6655 | 2250 | 1626 | 72.2667 | |
| anovak-vg | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 96.7565 | 97.0533 | 96.4614 | 41.7715 | 2075 | 63 | 2099 | 77 | 36 | 46.7532 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 97.8571 | 96.4789 | 99.2754 | 41.7722 | 137 | 5 | 137 | 1 | 1 | 100.0000 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 97.8571 | 96.4789 | 99.2754 | 41.7722 | 137 | 5 | 137 | 1 | 1 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | * | hetalt | 94.7356 | 90.7915 | 99.0379 | 41.7792 | 1755 | 178 | 1750 | 17 | 17 | 100.0000 | |
| qzeng-custom | INDEL | C16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 0.0000 | 0.0000 | 41.7808 | 0 | 0 | 0 | 85 | 0 | 0.0000 | ||
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 57.0043 | 54.0284 | 60.3272 | 41.7857 | 114 | 97 | 295 | 194 | 159 | 81.9588 | |
| qzeng-custom | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.7726 | 99.6365 | 99.9090 | 41.7859 | 2193 | 8 | 2195 | 2 | 1 | 50.0000 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 71.6357 | 72.7045 | 70.5979 | 41.7864 | 7530 | 2827 | 9069 | 3777 | 3029 | 80.1959 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.5220 | 86.1761 | 99.8768 | 41.7921 | 773 | 124 | 811 | 1 | 1 | 100.0000 | |
| anovak-vg | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 96.2926 | 96.8040 | 95.7866 | 41.7994 | 10389 | 343 | 10503 | 462 | 244 | 52.8139 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.3529 | 89.7315 | 95.1320 | 41.7997 | 2473 | 283 | 2775 | 142 | 134 | 94.3662 | |
| qzeng-custom | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.4064 | 99.1978 | 99.6159 | 41.7997 | 7296 | 59 | 7261 | 28 | 6 | 21.4286 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0811 | 99.3345 | 98.8289 | 41.8039 | 18062 | 121 | 18059 | 214 | 2 | 0.9346 | |
| jli-custom | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.8864 | 99.9091 | 99.8638 | 41.8076 | 2199 | 2 | 2199 | 3 | 2 | 66.6667 | |
| gduggal-snapvard | SNP | tv | HG002compoundhet | homalt | 90.8698 | 84.7107 | 97.9946 | 41.8088 | 2870 | 518 | 2541 | 52 | 38 | 73.0769 | |
| jpowers-varprowl | INDEL | I1_5 | HG002complexvar | homalt | 96.2923 | 95.8879 | 96.7001 | 41.8106 | 12895 | 553 | 12835 | 438 | 379 | 86.5297 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.2176 | 96.6110 | 97.8319 | 41.8109 | 19898 | 698 | 19899 | 441 | 420 | 95.2381 | |
| hfeng-pmm3 | SNP | tv | tech_badpromoters | het | 98.4615 | 96.9697 | 100.0000 | 41.8182 | 32 | 1 | 32 | 0 | 0 | ||
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 50.6627 | 34.2063 | 97.6335 | 41.8233 | 2769 | 5326 | 3053 | 74 | 71 | 95.9459 | |
| raldana-dualsentieon | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9319 | 99.9546 | 99.9092 | 41.8384 | 2200 | 1 | 2200 | 2 | 2 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 100.0000 | 100.0000 | 100.0000 | 41.8452 | 1330 | 0 | 1330 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 100.0000 | 100.0000 | 100.0000 | 41.8452 | 1330 | 0 | 1330 | 0 | 0 | ||
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9319 | 100.0000 | 99.8639 | 41.8470 | 2201 | 0 | 2201 | 3 | 3 | 100.0000 | |
| ckim-isaac | INDEL | I6_15 | * | homalt | 87.6777 | 79.9968 | 96.9903 | 41.8473 | 4991 | 1248 | 4995 | 155 | 121 | 78.0645 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 84.7448 | 77.6461 | 93.2722 | 41.8494 | 917 | 264 | 915 | 66 | 66 | 100.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 84.3708 | 77.0533 | 93.2238 | 41.8507 | 910 | 271 | 908 | 66 | 66 | 100.0000 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 85.7805 | 75.7534 | 98.8670 | 41.8516 | 1659 | 531 | 1658 | 19 | 17 | 89.4737 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 94.6679 | 92.1212 | 97.3595 | 41.8524 | 304 | 26 | 1143 | 31 | 26 | 83.8710 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 62.8790 | 57.8527 | 68.8617 | 41.8554 | 7975 | 5810 | 7937 | 3589 | 3504 | 97.6317 | |
| eyeh-varpipe | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.7872 | 99.8789 | 97.7191 | 41.8567 | 2475 | 3 | 2442 | 57 | 4 | 7.0175 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 50.2633 | 93.9024 | 34.3158 | 41.8605 | 77 | 5 | 163 | 312 | 287 | 91.9872 | |
| ghariani-varprowl | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 98.2390 | 100.0000 | 96.5390 | 41.8664 | 1311 | 0 | 1311 | 47 | 32 | 68.0851 | |
| jmaeng-gatk | SNP | * | HG002compoundhet | * | 99.3502 | 98.8847 | 99.8202 | 41.8705 | 25534 | 288 | 25531 | 46 | 39 | 84.7826 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 100.0000 | 100.0000 | 100.0000 | 41.8733 | 211 | 0 | 211 | 0 | 0 | ||
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.8579 | 98.3570 | 99.3639 | 41.8770 | 17959 | 300 | 17963 | 115 | 109 | 94.7826 | |
| asubramanian-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.4506 | 98.8726 | 98.0323 | 41.8823 | 17978 | 205 | 17985 | 361 | 4 | 1.1080 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.7466 | 97.5243 | 100.0000 | 41.8848 | 1103 | 28 | 1110 | 0 | 0 | ||
| mlin-fermikit | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.3026 | 99.5107 | 97.1234 | 41.8851 | 6712 | 33 | 6719 | 199 | 180 | 90.4523 | |
| jmaeng-gatk | INDEL | I6_15 | func_cds | * | 97.6744 | 97.6744 | 97.6744 | 41.8919 | 42 | 1 | 42 | 1 | 0 | 0.0000 | |
| ckim-dragen | SNP | ti | tech_badpromoters | het | 98.8506 | 97.7273 | 100.0000 | 41.8919 | 43 | 1 | 43 | 0 | 0 | ||