{"id":"W2145636602","doi":"10.1093/bioinformatics/btq092","title":"High quality SNP calling using Illumina data at shallow coverage","year":2010,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":55,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Cancer Agency","funders":"","keywords":"Single-nucleotide polymorphism; SNP; Genome; Reference genome; Software; Computer science; Computational biology; Data mining; Genetics; Biology; Gene; 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":[0.000358437,0.0001684204,0.0001851076,0.00002213251,0.0001920341,0.00003761202,0.000449297,0.0001601906,0.00002337698],"category_scores_gemma":[0.000143278,0.0001546431,0.00005591754,0.00004581494,0.00009940068,0.000003585883,0.0008978586,0.0001092208,0.00002248064],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001367375,"about_ca_system_score_gemma":0.00007263764,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001095903,"about_ca_topic_score_gemma":0.0003797494,"domain_scores_codex":[0.9989681,0.00001617896,0.0003953419,0.0002147665,0.0001457263,0.0002598518],"domain_scores_gemma":[0.9986568,0.0000197433,0.0001787039,0.0009841444,0.00007149318,0.00008908057],"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":[0.00004322963,0.00004665632,0.009270504,0.00008774042,0.0001245122,0.000001659373,0.0002676173,0.0002970251,0.9835904,0.0003748936,0.001341583,0.004554196],"study_design_scores_gemma":[0.004174588,0.0005680878,0.08285879,0.00005949309,0.0003043405,0.0001703444,0.001034927,0.05912187,0.3116613,0.0007127991,0.5362922,0.0030413],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9948426,0.0001685277,0.002793658,0.0000422289,0.000544282,0.0001340104,0.0003432911,0.000006143216,0.001125264],"genre_scores_gemma":[0.9623852,0.0001814992,0.03624902,0.0002654287,0.0002869324,0.000002466486,0.0004343856,0.00001710782,0.0001779831],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6719291,"threshold_uncertainty_score":0.6306161,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05956912626817135,"score_gpt":0.3044715002253539,"score_spread":0.2449023739571825,"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."}}