{"id":"W2771784697","doi":"10.24870/cjb.2017-a210","title":"A validated pipeline for detection of SNVs and short InDels from RNA Sequencing","year":2017,"lang":"en","type":"article","venue":"Canadian Journal of Biotechnology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"","keywords":"Computational biology; Indel; Biology; RNA; Genetics; Reference genome; Pipeline (software); DNA sequencing; Computer science; Gene; Genotype; Single-nucleotide polymorphism","routes":{"ca_aff":false,"ca_fund":false,"ca_venue":true,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001329068,0.00007734042,0.0001712529,0.0001018529,0.000146296,0.00001616821,0.0002120486,0.0002479673,0.000001528739],"category_scores_gemma":[0.0002161453,0.00007433959,0.00005215238,0.00001963638,0.0002096034,0.000001324399,0.00003495302,0.00008483669,1.082986e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002071203,"about_ca_system_score_gemma":0.0002273675,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002450085,"about_ca_topic_score_gemma":0.01563765,"domain_scores_codex":[0.9994902,0.000009267663,0.0002111977,0.0001181906,0.00002706486,0.0001440921],"domain_scores_gemma":[0.9993476,0.000007743651,0.000202416,0.0002248471,0.0001243972,0.00009294332],"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":[0.00002260445,0.000001909066,0.001297202,0.000004321752,0.0000716692,0.000004371076,0.00003154987,0.000007241219,0.9748253,0.00002653199,0.00006185108,0.0236454],"study_design_scores_gemma":[0.0003220561,0.0002709932,0.003321999,0.00001369971,0.00003675563,0.00004576728,0.0001281744,0.00006895068,0.9884179,0.0007548816,0.006541054,0.00007774411],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9915302,0.002222919,0.005365609,0.0004885505,0.000204905,0.00007435107,0.00007907351,7.036884e-7,0.00003370942],"genre_scores_gemma":[0.9984514,0.0003420695,0.001023376,0.00003894295,0.0001178141,0.000001635072,0.00000378171,0.000008870055,0.00001210542],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02356766,"threshold_uncertainty_score":0.8726174,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02129060198095129,"score_gpt":0.2399485742593545,"score_spread":0.2186579722784032,"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."}}