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
.rst
.pdf
sgkit.variables.variant_beta_spec
¶
sgkit.variables.
variant_beta_spec
=
ArrayLikeSpec(default_name='variant_beta',
kind=None,
ndim=None)
¶
Beta values associated with each variant and trait.
sgkit.variables.variant_allele_total_spec
sgkit.variables.variant_call_rate_spec