Index

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_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) concat_zarrs() (in module sgkit.io.vcf) 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) covariates_spec (in module sgkit.variables)

D

display_genotypes() (in module sgkit) divergence() (in module sgkit)

diversity() (in module sgkit) dosage_spec (in module sgkit.variables)

F

filter_partial_calls() (in module sgkit)

Fst() (in module sgkit)

G

Garud_H() (in module sgkit)

genotype_count_spec (in module sgkit.variables) gwas_linear_regression() (in module sgkit)

H

hardy_weinberg_test() (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)

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

partition_into_regions() (in module sgkit.io.vcf) pbs() (in module sgkit)

pc_relate() (in module sgkit) pc_relate_phi_spec (in module sgkit.variables)

R

read_bgen() (in module sgkit.io.bgen) read_plink() (in module sgkit.io.plink) read_scikit_allel_vcfzarr() (in module sgkit) 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_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_identity_by_state_spec (in module sgkit.variables) stat_observed_heterozygosity_spec (in module sgkit.variables) stat_pbs_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_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) vcf_to_zarr() (in module sgkit.io.vcf) vcf_to_zarrs() (in module sgkit.io.vcf)

W

Weir_Goudet_beta() (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)