{"id":"W4380608088","doi":"10.1101/2023.06.13.544861","title":"SNPLift: Fast and accurate conversion of genetic variant coordinates across genome assemblies","year":2023,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université Laval","funders":"Government of Canada; Université Laval; Grain Farmers of Ontario; Génome Québec; Canadian Field Crop Research Alliance; Genome Canada","keywords":"Indel; Reference genome; Genome; Computational biology; Computer science; Biology; Genomics; Genetics; Single-nucleotide polymorphism; Genotype; Gene","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.003740669,0.002132565,0.001429154,0.003026681,0.001078246,0.001949894,0.002445885,0.001175439,0.006537531],"category_scores_gemma":[0.009828222,0.001182924,0.001468395,0.002384599,0.000545095,0.001735229,0.001531249,0.002378809,0.005479376],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000689442,"about_ca_system_score_gemma":0.001227745,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003694344,"about_ca_topic_score_gemma":0.004042694,"domain_scores_codex":[0.9975747,0.0003543952,0.0002474428,0.0008409125,0.0008395459,0.0001429096],"domain_scores_gemma":[0.9962714,0.001449044,0.0006113544,0.0007082981,0.0007940592,0.0001658576],"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":[0.002277733,0.0004187438,0.01982469,0.002098496,0.001097965,0.001581894,0.00086543,0.04059198,0.2054603,0.005465244,0.1950719,0.5252457],"study_design_scores_gemma":[0.000669684,0.0006337236,0.01703516,0.0004094934,0.0002974216,0.001808831,0.0003093776,0.5112436,0.341973,0.01067365,0.114395,0.0005512054],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.05585015,0.001209652,0.6301057,0.0004968706,0.0005206935,0.0004200408,0.03530014,0.273131,0.002965787],"genre_scores_gemma":[0.1289919,0.0004713842,0.7832944,0.0004466625,0.0001412899,0.0007399384,0.07032666,0.01305916,0.002528577],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.006537531,"threshold_uncertainty_score":0.0218702,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01569257804153083,"score_gpt":0.2337966734048539,"score_spread":0.218104095363323,"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."}}