{"id":"W4410975639","doi":"10.1093/gigascience/giaf049","title":"Analysis-ready VCF at Biobank scale using Zarr","year":2025,"lang":"en","type":"article","venue":"GigaScience","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; Ontario Genomics","funders":"National Human Genome Research Institute; Knut och Alice Wallenbergs Stiftelse; Wellcome Trust; Bill and Melinda Gates Foundation","keywords":"Computer science; Biobank; Scalability; Terabyte; Data mining; Big data; Encoding (memory); Field (mathematics); Database; Bioinformatics; Artificial intelligence","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":[0.0001465918,0.0001008058,0.0001261445,0.00008199767,0.000235969,0.00002503602,0.0002523772,0.00005402908,0.0000102457],"category_scores_gemma":[0.00002401628,0.00009258035,0.0001202617,0.0005082614,0.0001895391,6.490777e-7,0.0003002511,0.000027371,0.000007645735],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002156666,"about_ca_system_score_gemma":0.00006482885,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005885966,"about_ca_topic_score_gemma":0.000178448,"domain_scores_codex":[0.9991546,0.00001893177,0.0001296338,0.0003736698,0.00009233963,0.0002308179],"domain_scores_gemma":[0.9995074,0.000006567221,0.00004262073,0.0003347733,0.00006215655,0.00004650249],"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":[0.000007727995,0.00001125776,0.1298951,0.000003339462,0.0001127345,5.373166e-7,0.00003073552,0.001338843,0.8675337,0.00006293138,0.0002326708,0.0007703939],"study_design_scores_gemma":[0.000494056,0.0001401825,0.3819046,0.00001382109,0.0005644027,0.000008893362,0.0001830798,0.004785123,0.5510836,0.0002838132,0.06001721,0.0005212211],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9926077,0.001755461,0.002000731,0.00008865233,0.000199741,0.0000650932,0.00001643047,0.000003221608,0.00326299],"genre_scores_gemma":[0.9961755,0.0001107525,0.001248848,0.000299489,0.00004502834,0.000002784821,0.000009484887,0.000003816377,0.002104285],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3164502,"threshold_uncertainty_score":0.3775317,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01347740047657392,"score_gpt":0.2740052126660191,"score_spread":0.2605278121894452,"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."}}