Index B | C | D | F | G | H | I | L | M | O | P | R | S | T | V | W | Z B bgen_to_zarr() (in module sgkit.io.bgen) C call_allele_count_spec (in module sgkit.variables) call_allele_frequencies() (in module sgkit) call_allele_frequency_spec (in module sgkit.variables) call_dosage_mask_spec (in module sgkit.variables) call_dosage_spec (in module sgkit.variables) call_genotype_complete_mask_spec (in module sgkit.variables) call_genotype_complete_spec (in module sgkit.variables) call_genotype_fill_spec (in module sgkit.variables) call_genotype_index_mask_spec (in module sgkit.variables) call_genotype_index_spec (in module sgkit.variables) call_genotype_mask_spec (in module sgkit.variables) call_genotype_phased_spec (in module sgkit.variables) call_genotype_probability_mask_spec (in module sgkit.variables) call_genotype_probability_spec (in module sgkit.variables) call_genotype_spec (in module sgkit.variables) call_heterozygosity_spec (in module sgkit.variables) call_ploidy_spec (in module sgkit.variables) cohort_allele_count_spec (in module sgkit.variables) cohort_allele_frequencies() (in module sgkit) cohort_allele_frequency_spec (in module sgkit.variables) convert_call_to_index() (in module sgkit) convert_probability_to_call() (in module sgkit) count_call_alleles() (in module sgkit) count_cohort_alleles() (in module sgkit) count_variant_alleles() (in module sgkit) count_variant_genotypes() (in module sgkit) covariates_spec (in module sgkit.variables) D display_genotypes() (in module sgkit) display_pedigree() (in module sgkit) divergence() (in module sgkit) diversity() (in module sgkit) F filter_partial_calls() (in module sgkit) Fst() (in module sgkit) G Garud_H() (in module sgkit) genee() (in module sgkit) genomic_relationship() (in module sgkit) gwas_linear_regression() (in module sgkit) H hardy_weinberg_test() (in module sgkit) hybrid_inverse_relationship() (in module sgkit) hybrid_relationship() (in module sgkit) I identity_by_state() (in module sgkit) individual_heterozygosity() (in module sgkit) infer_call_ploidy() (in module sgkit) infer_sample_ploidy() (in module sgkit) infer_variant_ploidy() (in module sgkit) interval_contig_name_spec (in module sgkit.variables) interval_start_spec (in module sgkit.variables) interval_stop_spec (in module sgkit.variables) invert_relationship_matrix() (in module sgkit) L ld_matrix() (in module sgkit) ld_prune() (in module sgkit) ld_prune_index_to_drop_spec (in module sgkit.variables) load_dataset() (in module sgkit) M maximal_independent_set() (in module sgkit) O observed_heterozygosity() (in module sgkit) P pairwise_distance() (in module sgkit) parent_id_spec (in module sgkit.variables) parent_indices() (in module sgkit) parent_spec (in module sgkit.variables) pbs() (in module sgkit) pc_relate() (in module sgkit) pc_relate_phi_spec (in module sgkit.variables) pedigree_contribution() (in module sgkit) pedigree_inbreeding() (in module sgkit) pedigree_inverse_kinship() (in module sgkit) pedigree_kinship() (in module sgkit) pedigree_sel() (in module sgkit) plink_to_zarr() (in module sgkit.io.plink) R read_bgen() (in module sgkit.io.bgen) read_plink() (in module sgkit.io.plink) rechunk_bgen() (in module sgkit.io.bgen) regenie() (in module sgkit) regenie_base_prediction_spec (in module sgkit.variables) regenie_loco_prediction_spec (in module sgkit.variables) regenie_meta_prediction_spec (in module sgkit.variables) S sample_call_rate_spec (in module sgkit.variables) sample_cohort_spec (in module sgkit.variables) sample_id_spec (in module sgkit.variables) sample_n_called_spec (in module sgkit.variables) sample_n_het_spec (in module sgkit.variables) sample_n_hom_alt_spec (in module sgkit.variables) sample_n_hom_ref_spec (in module sgkit.variables) sample_n_non_ref_spec (in module sgkit.variables) sample_pca_component_spec (in module sgkit.variables) sample_pca_explained_variance_ratio_spec (in module sgkit.variables) sample_pca_explained_variance_spec (in module sgkit.variables) sample_pca_loading_spec (in module sgkit.variables) sample_pca_projection_spec (in module sgkit.variables) sample_ploidy_spec (in module sgkit.variables) sample_stats() (in module sgkit) save_dataset() (in module sgkit) simulate_genedrop() (in module sgkit) simulate_genotype_call_dataset() (in module sgkit) stat_divergence_spec (in module sgkit.variables) stat_diversity_spec (in module sgkit.variables) stat_Fst_spec (in module sgkit.variables) stat_Garud_h123_spec (in module sgkit.variables) stat_Garud_h12_spec (in module sgkit.variables) stat_Garud_h1_spec (in module sgkit.variables) stat_Garud_h2_h1_spec (in module sgkit.variables) stat_genomic_kinship_spec (in module sgkit.variables) stat_genomic_relationship_spec (in module sgkit.variables) stat_Hamilton_Kerr_lambda_spec (in module sgkit.variables) stat_Hamilton_Kerr_tau_spec (in module sgkit.variables) stat_hybrid_inverse_relationship_spec (in module sgkit.variables) stat_hybrid_relationship_spec (in module sgkit.variables) stat_identity_by_state_spec (in module sgkit.variables) stat_inverse_relationship_spec (in module sgkit.variables) stat_observed_heterozygosity_spec (in module sgkit.variables) stat_pbs_spec (in module sgkit.variables) stat_pedigree_contribution_spec (in module sgkit.variables) stat_pedigree_inbreeding_spec (in module sgkit.variables) stat_pedigree_inverse_kinship_spec (in module sgkit.variables) stat_pedigree_inverse_relationship_spec (in module sgkit.variables) stat_pedigree_kinship_spec (in module sgkit.variables) stat_pedigree_relationship_spec (in module sgkit.variables) stat_Tajimas_D_spec (in module sgkit.variables) stat_Weir_Goudet_beta_spec (in module sgkit.variables) T Tajimas_D() (in module sgkit) traits_spec (in module sgkit.variables) V variant_allele_count_spec (in module sgkit.variables) variant_allele_frequency_spec (in module sgkit.variables) variant_allele_spec (in module sgkit.variables) variant_allele_total_spec (in module sgkit.variables) variant_call_rate_spec (in module sgkit.variables) variant_contig_spec (in module sgkit.variables) variant_genotype_count_spec (in module sgkit.variables) variant_hwe_p_value_spec (in module sgkit.variables) variant_id_spec (in module sgkit.variables) variant_linreg_beta_spec (in module sgkit.variables) variant_linreg_p_value_spec (in module sgkit.variables) variant_linreg_t_value_spec (in module sgkit.variables) variant_n_called_spec (in module sgkit.variables) variant_n_het_spec (in module sgkit.variables) variant_n_hom_alt_spec (in module sgkit.variables) variant_n_hom_ref_spec (in module sgkit.variables) variant_n_non_ref_spec (in module sgkit.variables) variant_ploidy_spec (in module sgkit.variables) variant_position_spec (in module sgkit.variables) variant_score_spec (in module sgkit.variables) variant_stats() (in module sgkit) W Weir_Goudet_beta() (in module sgkit) window_by_genome() (in module sgkit) window_by_interval() (in module sgkit) window_by_position() (in module sgkit) window_by_variant() (in module sgkit) window_contig_spec (in module sgkit.variables) window_start_spec (in module sgkit.variables) window_stop_spec (in module sgkit.variables) write_plink() (in module sgkit.io.plink) Z zarr_to_plink() (in module sgkit.io.plink)
