{"id":"W4402343843","doi":"10.1101/2024.09.04.611267","title":"Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline","year":2024,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Jonsson Comprehensive Cancer Center; U.S. National Library of Medicine; Canadian Institutes of Health Research; UCLA Health System; Prostate Cancer Foundation; National Institutes of Health; American Society of Clinical Oncology; U.S. Department of Defense","keywords":"Germline; Somatic cell; Pipeline (software); Genomics; Computational biology; Genetics; Biology; Computer science; Genome; Gene","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002982778,0.001185024,0.0007126895,0.00113035,0.0008280472,0.001825805,0.002209683,0.001051932,0.01087352],"category_scores_gemma":[0.003209781,0.001223761,0.001350192,0.0008538984,0.0005176984,0.001522869,0.002169527,0.002438911,0.005100009],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001224153,"about_ca_system_score_gemma":0.002779989,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003400865,"about_ca_topic_score_gemma":0.003333282,"domain_scores_codex":[0.9990572,0.0001120815,0.00006030267,0.0003105979,0.0003346545,0.0001251935],"domain_scores_gemma":[0.999175,0.0002698434,0.00007291862,0.0001802249,0.0001816755,0.0001203457],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.002560557,0.0003163745,0.01067491,0.001281853,0.0008156608,0.0008973325,0.0009870561,0.04574496,0.3037567,0.03065946,0.1743082,0.427997],"study_design_scores_gemma":[0.0006979825,0.0003596572,0.005895631,0.0001737017,0.0002517384,0.0008755813,0.0001123935,0.392818,0.2527948,0.0569311,0.2886235,0.0004658785],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.0183912,0.0006905638,0.8092508,0.000612727,0.0002501748,0.0005172503,0.01204321,0.1529462,0.005297764],"genre_scores_gemma":[0.09867012,0.0005467698,0.8362748,0.0009850026,0.0001314471,0.001378834,0.03813839,0.01778537,0.006089272],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.01087352,"threshold_uncertainty_score":0.03637558,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01852966889889133,"score_gpt":0.2350057746354114,"score_spread":0.2164761057365201,"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."}}