{"id":"W4317438559","doi":"10.1101/gr.277075.122","title":"An efficient genotyper and star-allele caller for pharmacogenomics","year":2023,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":57,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Victoria","funders":"National Cancer Institute; Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs; Baylor College of Medicine","keywords":"Biology; Genotyping; Genetics; Computational biology; Personal genomics; 1000 Genomes Project; DNA sequencing; Genomics; Copy-number variation; Massive parallel sequencing; Haplotype; Allele; Illumina dye sequencing; Genome; Genotype; Single-nucleotide polymorphism; Gene","routes":{"ca_aff":true,"ca_fund":true,"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":[0.006692892,0.001482718,0.001793666,0.001580072,0.0008517295,0.001783361,0.001764292,0.001889641,0.01032146],"category_scores_gemma":[0.01173608,0.001268704,0.001867778,0.001573436,0.0007233249,0.001580603,0.002083738,0.002500994,0.008376361],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007884691,"about_ca_system_score_gemma":0.002075188,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00146631,"about_ca_topic_score_gemma":0.003280467,"domain_scores_codex":[0.9949179,0.001514682,0.0003586391,0.001243892,0.00177684,0.0001881147],"domain_scores_gemma":[0.9934263,0.003282187,0.0007241017,0.001415343,0.0009013627,0.0002508145],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.003095941,0.0003546814,0.01387724,0.001328651,0.001101395,0.000491544,0.0004582916,0.0375913,0.2934033,0.01254922,0.04104165,0.5947069],"study_design_scores_gemma":[0.0004792163,0.001023041,0.01414003,0.0001157876,0.000380167,0.002185241,0.0001011232,0.4670075,0.3889184,0.01592316,0.1092189,0.0005072952],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.01131982,0.0004072605,0.9553781,0.0001901531,0.0001120503,0.0002088053,0.003236883,0.02779097,0.001356045],"genre_scores_gemma":[0.02766852,0.0002023189,0.9621302,0.0003383673,0.00004440965,0.0003664615,0.004084759,0.002532856,0.002632027],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01032146,"threshold_uncertainty_score":0.0353958,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0779488907613237,"score_gpt":0.3898485420644416,"score_spread":0.3118996513031179,"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."}}