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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
101-150 / 86044 show all | |||||||||||||||
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 50.2628 | 41.8345 | 62.9440 | 73.1508 | 18129 | 25206 | 21603 | 12718 | 4309 | 33.8811 | |
| gduggal-bwavard | INDEL | * | * | hetalt | 0.0000 | 0.4042 | 0.0000 | 0.0000 | 102 | 25135 | 0 | 0 | 0 | ||
| anovak-vg | SNP | ti | * | het | 98.0963 | 98.0413 | 98.1515 | 22.3908 | 1256788 | 25109 | 1253632 | 23610 | 9204 | 38.9835 | |
| gduggal-bwavard | INDEL | * | HG002compoundhet | hetalt | 0.0000 | 0.3892 | 0.0000 | 0.0000 | 98 | 25082 | 0 | 0 | 0 | ||
| jpowers-varprowl | INDEL | * | * | hetalt | 0.0000 | 0.7648 | 0.0000 | 0.0000 | 193 | 25044 | 0 | 0 | 0 | ||
| ghariani-varprowl | INDEL | * | * | hetalt | 0.0000 | 0.8995 | 0.0000 | 0.0000 | 227 | 25010 | 0 | 0 | 0 | ||
| jpowers-varprowl | INDEL | * | HG002compoundhet | hetalt | 0.0000 | 0.7625 | 0.0000 | 0.0000 | 192 | 24988 | 0 | 0 | 0 | ||
| ghariani-varprowl | INDEL | * | HG002compoundhet | hetalt | 0.0000 | 0.8975 | 0.0000 | 0.0000 | 226 | 24954 | 0 | 0 | 0 | ||
| ghariani-varprowl | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 74.4538 | 73.6260 | 75.3005 | 77.0932 | 69539 | 24910 | 69470 | 22787 | 21717 | 95.3043 | |
| gduggal-snapvard | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 74.9320 | 73.6508 | 76.2585 | 70.2157 | 69561 | 24886 | 122035 | 37993 | 31398 | 82.6415 | |
| asubramanian-gatk | SNP | * | map_l100_m2_e1 | het | 64.0057 | 47.1171 | 99.7652 | 87.0062 | 22097 | 24801 | 22091 | 52 | 14 | 26.9231 | |
| gduggal-bwaplat | SNP | tv | * | * | 98.5599 | 97.4574 | 99.6876 | 31.4101 | 945035 | 24655 | 945254 | 2962 | 440 | 14.8548 | |
| asubramanian-gatk | SNP | * | map_l100_m2_e0 | het | 63.7840 | 46.8782 | 99.7614 | 87.0574 | 21751 | 24648 | 21745 | 52 | 14 | 26.9231 | |
| gduggal-bwaplat | SNP | * | * | homalt | 98.9364 | 97.9135 | 99.9810 | 18.7279 | 1155537 | 24624 | 1155217 | 220 | 194 | 88.1818 | |
| asubramanian-gatk | SNP | * | map_l100_m1_e0 | het | 63.0315 | 46.0636 | 99.7898 | 86.5707 | 20894 | 24465 | 20888 | 44 | 12 | 27.2727 | |
| ciseli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 73.7262 | 74.1156 | 73.3408 | 74.2090 | 70000 | 24447 | 70171 | 25507 | 16983 | 66.5817 | |
| ckim-isaac | SNP | ti | map_siren | * | 86.1284 | 75.6983 | 99.8922 | 49.9174 | 75967 | 24388 | 75975 | 82 | 16 | 19.5122 | |
| ciseli-custom | INDEL | * | * | hetalt | 0.0000 | 3.4156 | 0.0000 | 0.0000 | 862 | 24375 | 0 | 0 | 0 | ||
| mlin-fermikit | SNP | ti | map_siren | * | 84.2869 | 75.7361 | 95.0143 | 45.5372 | 76005 | 24350 | 76001 | 3988 | 3501 | 87.7884 | |
| gduggal-snapvard | SNP | * | HG002complexvar | * | 97.8941 | 96.7741 | 99.0404 | 21.0357 | 730048 | 24336 | 708362 | 6863 | 2537 | 36.9663 | |
| ciseli-custom | INDEL | * | HG002compoundhet | hetalt | 0.0000 | 3.4114 | 0.0000 | 0.0000 | 859 | 24321 | 0 | 0 | 0 | ||
| gduggal-bwavard | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 75.4546 | 74.3184 | 76.6261 | 71.7256 | 70193 | 24256 | 70132 | 21393 | 20093 | 93.9232 | |
| astatham-gatk | SNP | * | * | * | 99.5934 | 99.2091 | 99.9807 | 19.0428 | 3030461 | 24158 | 3030315 | 584 | 162 | 27.7397 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 46.9190 | 44.4652 | 49.6593 | 57.4245 | 19269 | 24066 | 19242 | 19506 | 19313 | 99.0106 | |
| ckim-isaac | SNP | * | HG002complexvar | homalt | 95.6391 | 91.6604 | 99.9788 | 17.3239 | 264509 | 24066 | 264563 | 56 | 45 | 80.3571 | |
| asubramanian-gatk | SNP | * | map_l150_m2_e1 | * | 40.4494 | 25.3710 | 99.7071 | 94.4964 | 8172 | 24038 | 8169 | 24 | 6 | 25.0000 | |
| ckim-isaac | SNP | ti | * | homalt | 98.4855 | 97.0214 | 99.9944 | 13.4256 | 779120 | 23919 | 779153 | 44 | 32 | 72.7273 | |
| ckim-vqsr | SNP | ti | map_siren | * | 86.3605 | 76.1935 | 99.6585 | 68.7036 | 76464 | 23891 | 76451 | 262 | 25 | 9.5420 | |
| asubramanian-gatk | SNP | * | map_l150_m2_e0 | * | 40.2806 | 25.2386 | 99.7022 | 94.5086 | 8039 | 23813 | 8036 | 24 | 6 | 25.0000 | |
| astatham-gatk | SNP | * | * | het | 99.3521 | 98.7393 | 99.9725 | 20.1637 | 1849967 | 23620 | 1849845 | 508 | 95 | 18.7008 | |
| ckim-vqsr | SNP | * | * | homalt | 98.9894 | 98.0027 | 99.9961 | 17.7187 | 1156590 | 23571 | 1156567 | 45 | 41 | 91.1111 | |
| mlin-fermikit | SNP | * | map_l125_m2_e1 | * | 63.8417 | 50.2034 | 87.6540 | 61.8934 | 23697 | 23505 | 23692 | 3337 | 2934 | 87.9233 | |
| mlin-fermikit | SNP | * | map_l125_m2_e0 | * | 63.6201 | 49.9497 | 87.5929 | 61.7303 | 23338 | 23385 | 23333 | 3305 | 2908 | 87.9879 | |
| asubramanian-gatk | SNP | * | map_siren | homalt | 73.1014 | 57.6093 | 99.9906 | 63.4885 | 31775 | 23381 | 31766 | 3 | 2 | 66.6667 | |
| asubramanian-gatk | SNP | * | map_l150_m1_e0 | * | 38.6014 | 23.9309 | 99.7548 | 94.4087 | 7325 | 23284 | 7322 | 18 | 5 | 27.7778 | |
| anovak-vg | SNP | * | HG002complexvar | * | 97.6964 | 96.9184 | 98.4870 | 19.4533 | 731138 | 23247 | 712315 | 10943 | 8438 | 77.1087 | |
| qzeng-custom | SNP | * | * | * | 99.4966 | 99.2413 | 99.7533 | 22.5407 | 3031458 | 23176 | 3012983 | 7452 | 1530 | 20.5314 | |
| mlin-fermikit | SNP | * | map_l125_m1_e0 | * | 62.6787 | 48.9002 | 87.2681 | 57.2976 | 22165 | 23162 | 22160 | 3233 | 2859 | 88.4318 | |
| asubramanian-gatk | SNP | * | map_l100_m0_e0 | * | 45.8193 | 29.7342 | 99.8160 | 91.0946 | 9765 | 23076 | 9765 | 18 | 6 | 33.3333 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 41.5565 | 39.2117 | 44.1996 | 50.5594 | 14862 | 23040 | 14844 | 18740 | 18573 | 99.1089 | |
| gduggal-bwaplat | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 85.3226 | 75.6324 | 97.8608 | 79.5261 | 71434 | 23015 | 71409 | 1561 | 832 | 53.2992 | |
| ciseli-custom | SNP | ti | * | * | 98.3062 | 98.8974 | 97.7221 | 19.7040 | 2062524 | 22994 | 2057571 | 47963 | 7893 | 16.4564 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 77.5469 | 65.0258 | 96.0400 | 78.6649 | 42495 | 22856 | 42490 | 1752 | 879 | 50.1712 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 77.5469 | 65.0258 | 96.0400 | 78.6649 | 42495 | 22856 | 42490 | 1752 | 879 | 50.1712 | |
| asubramanian-gatk | SNP | ti | * | het | 99.0688 | 98.2225 | 99.9298 | 21.0842 | 1259105 | 22786 | 1259055 | 884 | 67 | 7.5792 | |
| ciseli-custom | SNP | * | HG002complexvar | * | 95.9712 | 96.9985 | 94.9655 | 20.7202 | 731742 | 22643 | 718679 | 38100 | 8358 | 21.9370 | |
| gduggal-snapplat | SNP | ti | * | * | 99.1814 | 98.9158 | 99.4485 | 24.4080 | 2062907 | 22611 | 2063333 | 11443 | 1808 | 15.8001 | |
| gduggal-snapvard | SNP | ti | * | * | 99.1158 | 98.9272 | 99.3052 | 22.3384 | 2063143 | 22374 | 2054412 | 14373 | 2372 | 16.5032 | |
| anovak-vg | INDEL | * | HG002complexvar | * | 72.8155 | 71.0364 | 74.6860 | 53.4026 | 54654 | 22284 | 56069 | 19004 | 16560 | 87.1395 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 50.3682 | 49.0920 | 51.7125 | 68.7841 | 21274 | 22061 | 21244 | 19837 | 19439 | 97.9936 | |