Index

B

base_prediction_spec (in module sgkit.variables)

C

call_allele_count_spec (in module sgkit.variables) call_dosage_mask_spec (in module sgkit.variables) call_dosage_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) 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

Fst() (in module sgkit)

G

Garud_h() (in module sgkit)

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

H

hardy_weinberg_test() (in module sgkit)

L

loco_prediction_spec (in module sgkit.variables)

M

meta_prediction_spec (in module sgkit.variables)

P

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

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

R

read_plink() (in module sgkit.io.plink)

read_vcfzarr() (in module sgkit) regenie() (in module sgkit)

S

sample_id_spec (in module sgkit.variables) sample_pcs_spec (in module sgkit.variables) simulate_genotype_call_dataset() (in module sgkit)

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)

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_beta_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_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_p_value_spec (in module sgkit.variables) variant_position_spec (in module sgkit.variables) variant_stats() (in module sgkit) variant_t_value_spec (in module sgkit.variables) vcf_to_zarr() (in module sgkit.io.vcf) vcf_to_zarrs() (in module sgkit.io.vcf)

W

window() (in module sgkit)

window_start_spec (in module sgkit.variables) window_stop_spec (in module sgkit.variables)

Z

zarrs_to_dataset() (in module sgkit.io.vcf)