{"id":"W2949930656","doi":"10.1534/g3.115.024596","title":"Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing Analysis","year":2016,"lang":"en","type":"article","venue":"G3 Genes Genomes Genetics","topic":"Genetic Mapping and Diversity in Plants and Animals","field":"Biochemistry, Genetics and Molecular Biology","cited_by":61,"is_retracted":false,"has_abstract":true,"ca_institutions":"Agriculture and Agri-Food Canada","funders":"","keywords":"Genotyping; Haplotype; Biology; Genome; Genomics; Computational biology; Polyploid; Reference genome; Single-nucleotide polymorphism; Locus (genetics); DNA sequencing; Genetics; Genotype; Computer science; 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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.000216757,0.000322508,0.0003327283,0.0001515782,0.0002612767,0.0000584426,0.0004338456,0.0002362354,0.00008465566],"category_scores_gemma":[0.00002886789,0.0002608646,0.0003264149,0.000262864,0.0001150085,0.000003507854,0.0001337506,0.0000408218,0.00003281318],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004100277,"about_ca_system_score_gemma":0.0002035492,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001194184,"about_ca_topic_score_gemma":0.00003956505,"domain_scores_codex":[0.9981234,0.00005052082,0.0003339751,0.0007066944,0.0002122625,0.0005731127],"domain_scores_gemma":[0.9986947,0.00005150314,0.0001620452,0.0006063396,0.0002818722,0.0002035433],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001103683,0.0000528172,0.03169747,0.00004814921,0.0007000357,0.00000222644,0.0000363654,0.002183336,0.7405529,0.00001886542,0.005916049,0.2186814],"study_design_scores_gemma":[0.00114564,0.0004836213,0.0009345135,0.00001691387,0.0005775026,0.000004238436,0.0000578484,0.0003904059,0.2392044,0.00008603613,0.7564358,0.0006630548],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.267664,0.2231831,0.5049621,0.0006143909,0.0004671036,0.0007384398,0.001832504,0.0001338462,0.0004046572],"genre_scores_gemma":[0.9383176,0.02449065,0.02954655,0.001295758,0.0005623893,0.00007396898,0.0008164203,0.00009080589,0.004805843],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.7505198,"threshold_uncertainty_score":0.9999844,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01838367195441515,"score_gpt":0.2326473485488382,"score_spread":0.2142636765944231,"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."}}