{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0007074188,0.0002891338,0.0004321845,0.0005318259,0.0002921258,0.0006769196,0.000390742,0.0003907055,0.001624453],"category_scores_gemma":[0.000998518,0.0004488497,0.0003216076,0.0004973659,0.0003563866,0.0005957636,0.0008920697,0.0008383768,0.0009113121],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003281901,"about_ca_system_score_gemma":0.0004370123,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008426553,"about_ca_topic_score_gemma":0.004271002,"domain_scores_codex":[0.9996492,0.00007253463,0.00001865439,0.0001264897,0.00009862028,0.00003438713],"domain_scores_gemma":[0.9994082,0.0002010678,0.00006958155,0.0002020965,0.00007083958,0.00004810024],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00005449187,0.00001116178,0.002674172,0.0001383923,0.00003846059,0.00004763946,0.0001135594,0.002388074,0.9673439,0.001536533,0.000367854,0.02528562],"study_design_scores_gemma":[0.00004430492,0.00016101,0.0551532,0.0001006467,0.00008941087,0.0007192894,0.0002655743,0.02878346,0.8718024,0.01107656,0.0317233,0.00008087572],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.366179,0.00153079,0.6171521,0.000308328,0.00006705429,0.0001433719,0.007472587,0.002163431,0.004983271],"genre_scores_gemma":[0.4518239,0.001383186,0.5373491,0.0002199415,0.00002684771,0.000164508,0.006433664,0.0005383844,0.002060448],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.001624453,"threshold_uncertainty_score":0.005434394,"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."}}