{"id":"W2951561991","doi":"10.1038/s41467-017-01389-4","title":"Dense and accurate whole-chromosome haplotyping of individual genomes","year":2017,"lang":"en","type":"article","venue":"Nature Communications","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":114,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; Terry Fox Research Institute; BC Cancer Agency","funders":"National Human Genome Research Institute; National Institutes of Health","keywords":"Haplotype; Genome; Haplotype estimation; Genomics; Biology; Computational biology; Genetics; Ploidy; Chromosome; DNA sequencing; Whole genome sequencing; Reference genome; 1000 Genomes Project; Allele; Gene; Single-nucleotide polymorphism; Genotype","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001271401,0.00008242957,0.000101837,0.00002527173,0.0003925778,0.00006253196,0.0009924335,0.0002194926,0.000002046646],"category_scores_gemma":[0.0001327044,0.00008074474,0.00004229888,0.00002225433,0.0002705478,0.000007870691,0.0004437925,0.000247732,0.000001525585],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000003549355,"about_ca_system_score_gemma":0.00003663951,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001203651,"about_ca_topic_score_gemma":0.0002394792,"domain_scores_codex":[0.9995376,0.00003950496,0.0001287664,0.0001324179,0.00006551006,0.00009622108],"domain_scores_gemma":[0.9982712,0.00002557005,0.0001238263,0.001455033,0.0000847792,0.00003955057],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00003484834,0.0001237004,0.03371436,0.00002571933,0.0001433773,7.420371e-7,0.0003290476,0.000004103362,0.9536052,0.001982406,0.001035888,0.009000571],"study_design_scores_gemma":[0.002110723,0.0002998816,0.3718168,0.0001195985,0.0002097506,0.0000410808,0.000275247,0.0003669942,0.1843603,0.0007679292,0.4389093,0.0007224628],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9772766,0.01934939,0.00009474372,0.001559198,0.0001210588,0.0001279444,0.000133781,0.0000109725,0.001326303],"genre_scores_gemma":[0.9946068,0.0022145,0.002663398,0.0001739578,0.00005037332,0.000006650244,0.0001695517,0.00001220619,0.0001025416],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.769245,"threshold_uncertainty_score":0.3292675,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03630888462606767,"score_gpt":0.3028568472343648,"score_spread":0.2665479626082971,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}