Contents:
Getting Started
User Guide
Reading VCF
API reference
sgkit.io.bgen.bgen_to_zarr
sgkit.io.bgen.read_bgen
sgkit.io.bgen.rechunk_bgen
sgkit.io.plink.read_plink
sgkit.io.vcf.vcf_to_zarr
sgkit.io.vcf.partition_into_regions
sgkit.io.vcf.vcf_to_zarrs
sgkit.io.vcf.zarrs_to_dataset
sgkit.read_vcfzarr
sgkit.load_dataset
sgkit.save_dataset
sgkit.count_call_alleles
sgkit.count_cohort_alleles
sgkit.count_variant_alleles
sgkit.divergence
sgkit.diversity
sgkit.Fst
sgkit.Garud_H
sgkit.gwas_linear_regression
sgkit.hardy_weinberg_test
sgkit.pc_relate
sgkit.regenie
sgkit.sample_stats
sgkit.Tajimas_D
sgkit.variant_stats
sgkit.convert_probability_to_call
sgkit.display_genotypes
sgkit.filter_partial_calls
sgkit.simulate_genotype_call_dataset
sgkit.window
sgkit.variables.base_prediction_spec
sgkit.variables.call_allele_count_spec
sgkit.variables.call_dosage_spec
sgkit.variables.call_dosage_mask_spec
sgkit.variables.call_genotype_complete_spec
sgkit.variables.call_genotype_complete_mask_spec
sgkit.variables.call_genotype_spec
sgkit.variables.call_genotype_mask_spec
sgkit.variables.call_genotype_phased_spec
sgkit.variables.call_genotype_probability_spec
sgkit.variables.call_genotype_probability_mask_spec
sgkit.variables.cohort_allele_count_spec
sgkit.variables.covariates_spec
sgkit.variables.dosage_spec
sgkit.variables.genotype_counts_spec
sgkit.variables.loco_prediction_spec
sgkit.variables.meta_prediction_spec
sgkit.variables.pc_relate_phi_spec
sgkit.variables.sample_call_rate_spec
sgkit.variables.sample_id_spec
sgkit.variables.sample_n_called_spec
sgkit.variables.sample_n_het_spec
sgkit.variables.sample_n_hom_alt_spec
sgkit.variables.sample_n_hom_ref_spec
sgkit.variables.sample_n_non_ref_spec
sgkit.variables.sample_pcs_spec
sgkit.variables.stat_divergence_spec
sgkit.variables.stat_diversity_spec
sgkit.variables.stat_Fst_spec
sgkit.variables.stat_Garud_h1_spec
sgkit.variables.stat_Garud_h12_spec
sgkit.variables.stat_Garud_h123_spec
sgkit.variables.stat_Garud_h2_h1_spec
sgkit.variables.stat_Tajimas_D_spec
sgkit.variables.traits_spec
sgkit.variables.variant_allele_spec
sgkit.variables.variant_allele_count_spec
sgkit.variables.variant_allele_frequency_spec
sgkit.variables.variant_allele_total_spec
sgkit.variables.variant_beta_spec
sgkit.variables.variant_call_rate_spec
sgkit.variables.variant_contig_spec
sgkit.variables.variant_hwe_p_value_spec
sgkit.variables.variant_id_spec
sgkit.variables.variant_n_called_spec
sgkit.variables.variant_n_het_spec
sgkit.variables.variant_n_hom_alt_spec
sgkit.variables.variant_n_hom_ref_spec
sgkit.variables.variant_n_non_ref_spec
sgkit.variables.variant_p_value_spec
sgkit.variables.variant_position_spec
sgkit.variables.variant_t_value_spec
sgkit.variables.window_start_spec
sgkit.variables.window_stop_spec
Contributing to sgkit
Index
B
|
C
|
D
|
F
|
G
|
H
|
L
|
M
|
P
|
R
|
S
|
T
|
V
|
W
|
Z
B
base_prediction_spec (in module sgkit.variables)
bgen_to_zarr() (in module sgkit.io.bgen)
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_complete_mask_spec (in module sgkit.variables)
call_genotype_complete_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)
cohort_allele_count_spec (in module sgkit.variables)
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_counts_spec (in module sgkit.variables)
gwas_linear_regression() (in module sgkit)
H
hardy_weinberg_test() (in module sgkit)
L
load_dataset() (in module sgkit)
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_bgen() (in module sgkit.io.bgen)
read_plink() (in module sgkit.io.plink)
read_vcfzarr() (in module sgkit)
rechunk_bgen() (in module sgkit.io.bgen)
regenie() (in module sgkit)
S
sample_call_rate_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_pcs_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_Tajimas_D_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)