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Contents
Getting Started
User Guide
Reading VCF
Examples
GWAS Tutorial
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.concat_zarrs
sgkit.read_scikit_allel_vcfzarr
sgkit.load_dataset
sgkit.save_dataset
sgkit.call_allele_frequencies
sgkit.cohort_allele_frequencies
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.identity_by_state
sgkit.individual_heterozygosity
sgkit.ld_matrix
sgkit.ld_prune
sgkit.maximal_independent_set
sgkit.observed_heterozygosity
sgkit.pbs
sgkit.pc_relate
sgkit.regenie
sgkit.sample_stats
sgkit.Tajimas_D
sgkit.variant_stats
sgkit.Weir_Goudet_beta
sgkit.convert_probability_to_call
sgkit.display_genotypes
sgkit.filter_partial_calls
sgkit.infer_call_ploidy
sgkit.infer_sample_ploidy
sgkit.infer_variant_ploidy
sgkit.simulate_genotype_call_dataset
sgkit.window_by_position
sgkit.window_by_variant
sgkit.variables.regenie_base_prediction_spec
sgkit.variables.call_allele_count_spec
sgkit.variables.call_allele_frequency_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_fill_spec
sgkit.variables.call_genotype_phased_spec
sgkit.variables.call_genotype_probability_spec
sgkit.variables.call_genotype_probability_mask_spec
sgkit.variables.call_heterozygosity_spec
sgkit.variables.call_ploidy_spec
sgkit.variables.cohort_allele_count_spec
sgkit.variables.cohort_allele_frequency_spec
sgkit.variables.covariates_spec
sgkit.variables.dosage_spec
sgkit.variables.genotype_count_spec
sgkit.variables.ld_prune_index_to_drop_spec
sgkit.variables.regenie_loco_prediction_spec
sgkit.variables.regenie_meta_prediction_spec
sgkit.variables.pc_relate_phi_spec
sgkit.variables.sample_call_rate_spec
sgkit.variables.sample_cohort_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_pca_component_spec
sgkit.variables.sample_pca_explained_variance_spec
sgkit.variables.sample_pca_explained_variance_ratio_spec
sgkit.variables.sample_pca_loading_spec
sgkit.variables.sample_pca_projection_spec
sgkit.variables.sample_ploidy_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_identity_by_state_spec
sgkit.variables.stat_observed_heterozygosity_spec
sgkit.variables.stat_pbs_spec
sgkit.variables.stat_Tajimas_D_spec
sgkit.variables.stat_Weir_Goudet_beta_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_linreg_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_linreg_p_value_spec
sgkit.variables.variant_ploidy_spec
sgkit.variables.variant_position_spec
sgkit.variables.variant_score_spec
sgkit.variables.variant_linreg_t_value_spec
sgkit.variables.window_contig_spec
sgkit.variables.window_start_spec
sgkit.variables.window_stop_spec
How do I …
Contributing to sgkit
About
.rst
.pdf
sgkit.variables.stat_identity_by_state_spec
sgkit.variables.stat_identity_by_state_spec
#
sgkit.variables.
stat_identity_by_state_spec
=
ArrayLikeSpec(default_name='stat_identity_by_state',
__doc__='\nPairwise
IBS
probabilities
among
all
samples.\n',
kind='f',
ndim=2)
#
Pairwise IBS probabilities among all samples.
