{"id":"W4402253482","doi":"10.1093/bioinformatics/btae391","title":"GGTyper: genotyping complex structural variants using short-read sequencing data","year":2024,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"Amgen (Canada)","funders":"Berlin Institute of Health","keywords":"Genotyping; Computer science; Computational biology; Genetics; Biology; Genotype; Gene","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":[0.0001242816,0.0001546121,0.0001164904,0.00005066528,0.0001305277,0.000161249,0.0003762712,0.0000922161,0.00004524166],"category_scores_gemma":[0.00003488329,0.0001344292,0.00005506149,0.0000851035,0.00004388432,0.00002348369,0.0004027006,0.00007033398,0.00002345059],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003600644,"about_ca_system_score_gemma":0.0002481583,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002312771,"about_ca_topic_score_gemma":0.00001382402,"domain_scores_codex":[0.999131,0.0000126503,0.0002798244,0.0002148014,0.0001138076,0.0002479009],"domain_scores_gemma":[0.9992297,0.000007555857,0.000036306,0.0005967374,0.00004177765,0.0000879755],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00009909982,0.000038825,0.001549621,0.001618542,0.0009957014,0.0001705596,0.001610501,0.005136513,0.8661082,0.001835372,0.0146717,0.1061653],"study_design_scores_gemma":[0.0001521037,0.00005103736,0.001074445,0.00008186243,0.000102029,0.0003151855,0.000578656,0.965502,0.002093979,0.0001020829,0.0295104,0.00043626],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9769155,0.002183044,0.01727773,0.00003377108,0.0007108682,0.0002165446,0.0008109632,0.0000598529,0.001791751],"genre_scores_gemma":[0.972511,0.0001001206,0.02476585,0.0001943741,0.0003338134,0.000001221142,0.002003014,0.0000254411,0.00006518827],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9603655,"threshold_uncertainty_score":0.5481864,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.09498124191876284,"score_gpt":0.3235446239675812,"score_spread":0.2285633820488184,"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."}}