{"id":"W4407190337","doi":"10.1093/bib/bbaf044","title":"Assessment of the functionality and usability of open-source rare variant analysis pipelines","year":2024,"lang":"en","type":"review","venue":"Briefings in Bioinformatics","topic":"Genetic Associations and Epidemiology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institut de Cardiologie de Montréal; Harvard University; Institut National de la Santé et de la Recherche Médicale; Hospital for Sick Children; University of North Carolina at Chapel Hill; Northeast Normal University; Regeneron Pharmaceuticals","keywords":"Computer science; Pipeline (software); Usability; Scalability; Pipeline transport; Flexibility (engineering); Exploit; Weighting; Data mining; Data science; Computational biology; Biology; Database; Medicine; Human–computer interaction; Engineering; Statistics; Computer security","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001344359,0.0002022706,0.001091953,0.0001045734,0.0000409141,0.00002729167,0.000428479,0.0003085343,0.000009448465],"category_scores_gemma":[0.0004780268,0.0001295598,0.0003963472,0.0005860931,0.0001703725,0.000004656902,0.0008721345,0.000174898,5.213689e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003419303,"about_ca_system_score_gemma":0.0003390229,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002780684,"about_ca_topic_score_gemma":0.0001111092,"domain_scores_codex":[0.99804,0.0001886232,0.001271201,0.0002244782,0.0001334807,0.000142167],"domain_scores_gemma":[0.9983813,0.0001116154,0.0008458337,0.0005269977,0.000104848,0.00002942595],"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":[0.00002049991,0.0005457676,0.06357991,0.06557824,0.00835505,0.000001388553,0.0005049718,0.001579067,0.00002132266,0.003808463,0.01514784,0.8408575],"study_design_scores_gemma":[0.0002250988,0.0000733945,0.02939271,0.001401858,0.003888912,0.00002071277,0.0001038327,0.004006716,0.000003635247,0.0003257876,0.9602387,0.0003186278],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.001696497,0.9872521,0.007979019,0.0002140344,0.0001910618,0.0009074068,0.0005324909,0.000005637961,0.001221771],"genre_scores_gemma":[0.003155505,0.9871967,0.008807737,0.0001525562,0.00003664317,0.0000395484,0.0003379891,0.0000148285,0.0002585162],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.9450909,"threshold_uncertainty_score":0.5283296,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03579617331467934,"score_gpt":0.3557221290692336,"score_spread":0.3199259557545542,"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."}}