Index

A

add_as_info_dict() (in module gnomad.utils.vcf) add_filters_expr() (in module gnomad.utils.filtering) add_gencode_transcript_annotations() (in module gnomad.utils.constraint) add_gks_va() (in module gnomad.utils.annotations) add_gks_vrs() (in module gnomad.utils.annotations) add_grpMaxFAF95_v4() (in module gnomad.resources.grch38.gnomad) add_most_severe_consequence_to_consequence() (in module gnomad.utils.vep) add_most_severe_csq_to_tc_within_vep_root() (in module gnomad.utils.vep) add_rank() (in module gnomad.variant_qc.evaluation) add_reference_sequence() (in module gnomad.utils.reference_genome) add_variant_type() (in module gnomad.utils.annotations) adjust_sex_ploidy() (in module gnomad.sample_qc.sex) adjust_vcf_incompatible_types() (in module gnomad.utils.vcf) adjusted_sex_ploidy_expr() (in module gnomad.sample_qc.sex) age_hists_expr() (in module gnomad.utils.annotations) agg_by_strata() (in module gnomad.utils.annotations) all_sites_an() (in module gnomad.resources.grch38.gnomad) ALLELE_TYPE_FIELDS (in module gnomad.utils.vcf) AMBIGUOUS_RELATIONSHIP (in module gnomad.sample_qc.relatedness) annotate_adj() (in module gnomad.utils.annotations)

annotate_allele_info() (in module gnomad.utils.annotations) annotate_and_index_source_mt_for_sex_ploidy() (in module gnomad.utils.annotations) annotate_downsamplings() (in module gnomad.utils.annotations) annotate_exploded_vep_for_constraint_groupings() (in module gnomad.utils.constraint) annotate_freq() (in module gnomad.utils.annotations) annotate_mutation_type() (in module gnomad.utils.constraint) annotate_sex() (in module gnomad.sample_qc.pipeline) annotate_with_ht() (in module gnomad.utils.annotations) annotate_with_mu() (in module gnomad.utils.constraint) annotation_type_in_vcf_info() (in module gnomad.utils.annotations) annotation_type_is_numeric() (in module gnomad.utils.annotations) apply_onnx_classification_model() (in module gnomad.sample_qc.ancestry) apply_rf_model() (in module gnomad.variant_qc.random_forest) apply_sklearn_classification_model() (in module gnomad.sample_qc.ancestry) AS_FIELDS (in module gnomad.utils.vcf) AS_VQSR_FIELDS (in module gnomad.utils.vcf) assemble_constraint_context_ht() (in module gnomad.utils.constraint) assign_platform_from_pcs() (in module gnomad.sample_qc.platform) assign_population_pcs() (in module gnomad.sample_qc.ancestry) AZURE_OPEN_DATASETS (gnomad.resources.config.GnomadPublicResourceSource attribute)

B

BaseResource (class in gnomad.resources.resource_utils) BaseVersionedResource (class in gnomad.resources.resource_utils) bi_allelic_expr() (in module gnomad.utils.annotations) bi_allelic_site_inbreeding_expr() (in module gnomad.utils.annotations) BlockMatrixResource (class in gnomad.resources.resource_utils) bm() (gnomad.resources.resource_utils.BlockMatrixResource method) (gnomad.resources.resource_utils.GnomadPublicBlockMatrixResource method)

build_coverage_model() (in module gnomad.utils.constraint) build_freq_stratification_list() (in module gnomad.utils.annotations) build_models() (in module gnomad.utils.constraint) build_plateau_models() (in module gnomad.utils.constraint) build_vcf_export_reference() (in module gnomad.utils.vcf)

C

calculate_raw_z_score() (in module gnomad.utils.constraint) calculate_raw_z_score_sd() (in module gnomad.utils.constraint) CELL_LINES (in module gnomad.utils.transcript_annotation) check_file_exists_raise_error() (in module gnomad.utils.file_utils) check_global_and_row_annot_lengths() (in module gnomad.assessment.validity_checks) check_ht_fields_for_spark() (in module gnomad.variant_qc.random_forest) check_raw_and_adj_callstats() (in module gnomad.assessment.validity_checks) check_sex_chr_metrics() (in module gnomad.assessment.validity_checks) clean_tissue_name_for_browser() (in module gnomad.utils.transcript_annotation) COHORTS_WITH_POP_STORED_AS_SUBPOP (in module gnomad.resources.grch38.gnomad) collapse_strand() (in module gnomad.utils.constraint) combine_functions() (in module gnomad.utils.filtering) compare_row_counts() (in module gnomad.assessment.validity_checks) compare_subset_freqs() (in module gnomad.assessment.validity_checks) compute_allele_number_per_ref_site() (in module gnomad.utils.sparse_mt) compute_binned_truth_sample_concordance() (in module gnomad.variant_qc.evaluation) compute_callrate_mt() (in module gnomad.sample_qc.platform) compute_coverage_stats() (in module gnomad.utils.sparse_mt) compute_expected_variants() (in module gnomad.utils.constraint) compute_freq_by_strata() (in module gnomad.utils.annotations) compute_grouped_binned_ht() (in module gnomad.variant_qc.evaluation) compute_last_ref_block_end() (in module gnomad.utils.sparse_mt) compute_missingness() (in module gnomad.assessment.validity_checks) compute_pli() (in module gnomad.utils.constraint)

compute_qc_metrics_residuals() (in module gnomad.sample_qc.filtering) compute_ranked_bin() (in module gnomad.variant_qc.evaluation) compute_related_samples_to_drop() (in module gnomad.sample_qc.relatedness) compute_stats_per_ref_site() (in module gnomad.utils.sparse_mt) compute_stratified_metrics_filter() (in module gnomad.sample_qc.filtering) compute_stratified_sample_qc() (in module gnomad.sample_qc.filtering) constraint() (in module gnomad.resources.grch37.gnomad) (in module gnomad.resources.grch38.gnomad) convert_sklearn_rf_to_onnx() (in module gnomad.sample_qc.ancestry) count_variants_by_group() (in module gnomad.utils.constraint) count_vep_annotated_variants_per_interval() (in module gnomad.assessment.validity_checks) coverage() (in module gnomad.resources.grch37.gnomad) (in module gnomad.resources.grch38.gnomad) COVERAGE_CUTOFF (in module gnomad.utils.constraint) coverage_tsv_path() (in module gnomad.resources.grch38.gnomad) create_binned_ht() (in module gnomad.variant_qc.pipeline) create_fake_pedigree() (in module gnomad.sample_qc.relatedness) create_frequency_bins_expr() (in module gnomad.utils.annotations) create_label_groups() (in module gnomad.utils.vcf) create_truth_sample_ht() (in module gnomad.variant_qc.evaluation) create_tx_annotation_by_region() (in module gnomad.utils.transcript_annotation) create_vds() (in module gnomad.utils.file_utils) CSQ_CODING (in module gnomad.utils.vep) CSQ_SPLICE (in module gnomad.utils.vep) CURRENT_VEP_VERSION (in module gnomad.utils.vep)

D

DataException default_compute_info() (in module gnomad.utils.sparse_mt) default_generate_gene_lof_matrix() (in module gnomad.assessment.summary_stats) default_generate_gene_lof_summary() (in module gnomad.assessment.summary_stats) default_lift_data() (in module gnomad.utils.liftover) default_version (gnomad.resources.resource_utils.BaseVersionedResource attribute)

densify_all_reference_sites() (in module gnomad.utils.sparse_mt) densify_sites() (in module gnomad.utils.sparse_mt) determine_nearest_neighbors() (in module gnomad.sample_qc.filtering) downsampling_counts_expr() (in module gnomad.utils.constraint) DOWNSAMPLINGS (in module gnomad.resources.grch38.gnomad) DUPLICATE_OR_TWINS (in module gnomad.sample_qc.relatedness)

E

ENTRIES (in module gnomad.utils.vcf) expected_file_extensions (gnomad.resources.resource_utils.BaseResource attribute) (gnomad.resources.resource_utils.BlockMatrixResource attribute) (gnomad.resources.resource_utils.ExpressionResource attribute) (gnomad.resources.resource_utils.MatrixTableResource attribute) (gnomad.resources.resource_utils.PedigreeResource attribute) (gnomad.resources.resource_utils.TableResource attribute) (gnomad.resources.resource_utils.VariantDatasetResource attribute)

explode_by_vep_annotation() (in module gnomad.utils.vep) explode_downsamplings_oe() (in module gnomad.utils.constraint) explode_duplicate_samples_ht() (in module gnomad.sample_qc.relatedness) ExpressionResource (class in gnomad.resources.resource_utils)

F

faf_expr() (in module gnomad.utils.annotations) FAF_POPS (in module gnomad.utils.vcf) file_exists() (in module gnomad.utils.file_utils) fill_missing_key_combinations() (in module gnomad.utils.annotations) filter_arrays_by_meta() (in module gnomad.utils.filtering) filter_by_frequency() (in module gnomad.utils.filtering) filter_by_numeric_expr_range() (in module gnomad.utils.filtering) filter_expression_ht_by_tissues() (in module gnomad.utils.transcript_annotation) filter_for_mu() (in module gnomad.utils.filtering) filter_low_conf_regions() (in module gnomad.utils.filtering) filter_ref_blocks() (in module gnomad.utils.sparse_mt) filter_rows_for_qc() (in module gnomad.sample_qc.pipeline) filter_to_adj() (in module gnomad.utils.filtering) filter_to_autosomes() (in module gnomad.utils.filtering)

filter_to_clinvar_pathogenic() (in module gnomad.utils.filtering) filter_to_gencode_cds() (in module gnomad.utils.filtering) filter_to_trios() (in module gnomad.sample_qc.relatedness) filter_vep_to_canonical_transcripts() (in module gnomad.utils.vep) filter_vep_to_gene_list() (in module gnomad.utils.vep) filter_vep_to_mane_select_transcripts() (in module gnomad.utils.vep) filter_vep_to_synonymous_variants() (in module gnomad.utils.vep) filter_vep_transcript_csqs() (in module gnomad.utils.vep) filter_vep_transcript_csqs_expr() (in module gnomad.utils.vep) filter_x_nonpar() (in module gnomad.utils.filtering) filter_y_nonpar() (in module gnomad.utils.filtering) FORMAT_DICT (in module gnomad.utils.vcf) freq_bin_expr() (in module gnomad.assessment.summary_stats) from_phred() (in module gnomad.utils.gen_stats) fs_from_sb() (in module gnomad.utils.annotations)

G

gaussian_mixture_model_karyotype_assignment() (in module gnomad.sample_qc.sex) gen_anc_faf_max_expr() (in module gnomad.utils.annotations) generate_filter_combinations() (in module gnomad.assessment.summary_stats) generate_freq_group_membership_array() (in module gnomad.utils.annotations) generate_sib_stats() (in module gnomad.variant_qc.pipeline) generate_sib_stats_expr() (in module gnomad.sample_qc.relatedness) generate_trio_stats() (in module gnomad.variant_qc.pipeline) generate_trio_stats_expr() (in module gnomad.sample_qc.relatedness) generic_field_check() (in module gnomad.assessment.validity_checks) generic_field_check_loop() (in module gnomad.assessment.validity_checks) get_adj_expr() (in module gnomad.utils.annotations) get_all_pop_lengths() (in module gnomad.utils.constraint) get_allele_number_agg_func() (in module gnomad.utils.sparse_mt) get_an_criteria() (in module gnomad.assessment.summary_stats) get_annotations_hists() (in module gnomad.utils.annotations) get_as_info_expr() (in module gnomad.utils.sparse_mt) get_chr_x_hom_alt_cutoffs() (in module gnomad.sample_qc.sex) get_columns_quantiles() (in module gnomad.variant_qc.random_forest) get_constraint_flags() (in module gnomad.utils.constraint) get_constraint_grouping_expr() (in module gnomad.utils.constraint) get_default_public_resource_source() (in module gnomad.resources.config) get_downsampling_freq_indices() (in module gnomad.utils.constraint) get_duplicated_samples() (in module gnomad.sample_qc.relatedness) get_duplicated_samples_ht() (in module gnomad.sample_qc.relatedness) get_expression_proportion() (in module gnomad.utils.transcript_annotation) get_features_importance() (in module gnomad.variant_qc.random_forest) get_file_stats() (in module gnomad.utils.file_utils) get_gq_dp_adj_expr() (in module gnomad.utils.annotations) get_het_ab_adj_expr() (in module gnomad.utils.annotations) get_het_hom_summary_dict() (in module gnomad.assessment.summary_stats) get_is_haploid_expr() (in module gnomad.utils.annotations) get_labels() (in module gnomad.variant_qc.random_forest) get_liftover_genome() (in module gnomad.utils.liftover) get_lowqual_expr() (in module gnomad.utils.annotations) get_median_and_mad_expr() (in module gnomad.utils.gen_stats) get_module_importable_resources() (in module gnomad.resources.import_resources) get_most_severe_consequence_expr() (in module gnomad.utils.vep) get_most_severe_consequence_for_summary() (in module gnomad.utils.vep) get_mu_annotation_expr() (in module gnomad.utils.constraint) get_ploidy_cutoffs() (in module gnomad.sample_qc.sex) get_qc_mt() (in module gnomad.sample_qc.pipeline) get_r_for_pair_of_variants() (in module gnomad.variant_qc.ld) get_r_human_readable() (in module gnomad.variant_qc.ld) get_r_within_gene() (in module gnomad.variant_qc.ld) get_r_within_gene_in_pop() (in module gnomad.variant_qc.ld) get_reference_genome() (in module gnomad.utils.reference_genome) get_reference_ht() (in module gnomad.utils.reference_genome) get_relationship_expr() (in module gnomad.sample_qc.relatedness) get_resources_descriptions() (in module gnomad.resources.import_resources) get_rf_runs() (in module gnomad.variant_qc.random_forest) get_rows_data() (in module gnomad.utils.plotting) get_run_data() (in module gnomad.variant_qc.random_forest) get_sex_expr() (in module gnomad.sample_qc.sex) get_site_info_expr() (in module gnomad.utils.sparse_mt) get_slope_int_relationship_expr() (in module gnomad.sample_qc.relatedness) get_summary_ac_dict() (in module gnomad.assessment.summary_stats) get_summary_counts() (in module gnomad.assessment.summary_stats) get_summary_counts_dict() (in module gnomad.assessment.summary_stats) get_summary_stats_csq_filter_expr() (in module gnomad.assessment.summary_stats) get_summary_stats_filter_group_meta() (in module gnomad.assessment.summary_stats) get_summary_stats_variant_filter_expr() (in module gnomad.assessment.summary_stats) get_tissues_to_exclude() (in module gnomad.utils.transcript_annotation) get_truth_ht() (in module gnomad.resources.grch37.reference_data) (in module gnomad.resources.grch38.reference_data) get_tx_expression_expr() (in module gnomad.assessment.summary_stats) get_vep_context() (in module gnomad.utils.vep) get_vep_help() (in module gnomad.utils.vep) GNOMAD (gnomad.resources.config.GnomadPublicResourceSource attribute) gnomad.assessment.summary_stats module gnomad.assessment.validity_checks module gnomad.resources.config module gnomad.resources.grch37.gnomad module gnomad.resources.grch37.gnomad_ld module

gnomad.resources.grch37.reference_data module gnomad.resources.grch38.gnomad module gnomad.resources.grch38.reference_data module gnomad.resources.import_resources module gnomad.resources.resource_utils module gnomad.sample_qc.ancestry module gnomad.sample_qc.filtering module gnomad.sample_qc.pipeline module gnomad.sample_qc.platform module gnomad.sample_qc.relatedness module gnomad.sample_qc.sex module gnomad.utils.annotations module gnomad.utils.constraint module gnomad.utils.file_utils module gnomad.utils.filtering module gnomad.utils.gen_stats module gnomad.utils.intervals module gnomad.utils.liftover module gnomad.utils.parse module gnomad.utils.plotting module gnomad.utils.reference_genome module gnomad.utils.release module gnomad.utils.slack module gnomad.utils.sparse_mt module gnomad.utils.transcript_annotation module gnomad.utils.vcf module gnomad.utils.vep module gnomad.variant_qc.evaluation module gnomad.variant_qc.ld module gnomad.variant_qc.pipeline module gnomad.variant_qc.random_forest module gnomad.variant_qc.training module gnomad_gks() (in module gnomad.resources.grch38.gnomad) GNOMAD_PUBLIC_BUCKETS (in module gnomad.resources.resource_utils) GnomadPublicBlockMatrixResource (class in gnomad.resources.resource_utils) GnomadPublicMatrixTableResource (class in gnomad.resources.resource_utils) GnomadPublicPedigreeResource (class in gnomad.resources.resource_utils) GnomadPublicResource (class in gnomad.resources.resource_utils) GnomadPublicResourceSource (class in gnomad.resources.config) GnomadPublicTableResource (class in gnomad.resources.resource_utils) GOOGLE_CLOUD_PUBLIC_DATASETS (gnomad.resources.config.GnomadPublicResourceSource attribute) GRCH37_to_GRCH38_CHAIN (in module gnomad.utils.liftover) GRCH38_TO_GRCH37_CHAIN (in module gnomad.utils.liftover) GROUPS (in module gnomad.resources.grch38.gnomad) (in module gnomad.utils.vcf)

H

he() (gnomad.resources.resource_utils.ExpressionResource method) hemi_expr() (in module gnomad.utils.annotations) HGDP_POPS (in module gnomad.resources.grch38.gnomad) HISTS (in module gnomad.utils.vcf)

ht() (gnomad.resources.resource_utils.GnomadPublicPedigreeResource method) (gnomad.resources.resource_utils.GnomadPublicTableResource method) (gnomad.resources.resource_utils.PedigreeResource method) (gnomad.resources.resource_utils.TableResource method) ht_to_rf_df() (in module gnomad.variant_qc.random_forest)

I

import_gencode() (in module gnomad.resources.resource_utils) import_resource() (gnomad.resources.resource_utils.BaseResource method) (gnomad.resources.resource_utils.BlockMatrixResource method) (gnomad.resources.resource_utils.ExpressionResource method) (gnomad.resources.resource_utils.MatrixTableResource method) (gnomad.resources.resource_utils.PedigreeResource method) (gnomad.resources.resource_utils.TableResource method) (gnomad.resources.resource_utils.VariantDatasetResource method)

import_sites_vcf() (in module gnomad.resources.resource_utils) impute_sex_ploidy() (in module gnomad.utils.sparse_mt) IN_SILICO_ANNOTATIONS_INFO_DICT (in module gnomad.utils.vcf) index_globals() (in module gnomad.utils.vcf) infer_families() (in module gnomad.sample_qc.relatedness) infer_sex_karyotype() (in module gnomad.sample_qc.pipeline) INFO_DICT (in module gnomad.utils.vcf) interval_length() (in module gnomad.utils.intervals) is_resource_available() (gnomad.resources.resource_utils.GnomadPublicResource method)

J

JOINT_REGION_FLAG_FIELDS (in module gnomad.utils.vcf)

L

ld_index() (in module gnomad.resources.grch37.gnomad_ld) ld_matrix() (in module gnomad.resources.grch37.gnomad_ld) ld_scores() (in module gnomad.resources.grch37.gnomad_ld) liftover() (in module gnomad.resources.grch37.gnomad) liftover_expr() (in module gnomad.utils.liftover)

liftover_using_gnomad_map() (in module gnomad.utils.liftover) linear_and_log_tabs() (in module gnomad.utils.plotting) load_model() (in module gnomad.variant_qc.random_forest) LOF_CSQ_SET (in module gnomad.utils.vep) LOFTEE_LABELS (in module gnomad.utils.vep) low_conf_regions_expr() (in module gnomad.utils.filtering)

M

main() (in module gnomad.resources.import_resources) make_combo_header_text() (in module gnomad.utils.vcf) make_faf_index_dict() (in module gnomad.utils.release) make_filters_expr_dict() (in module gnomad.assessment.validity_checks) make_freq_index_dict() (in module gnomad.utils.release) make_freq_index_dict_from_meta() (in module gnomad.utils.release) make_group_sum_expr_dict() (in module gnomad.assessment.validity_checks) make_hist_bin_edges_expr() (in module gnomad.utils.vcf) make_hist_dict() (in module gnomad.utils.vcf) make_info_dict() (in module gnomad.utils.vcf) make_label_combos() (in module gnomad.utils.vcf) make_vcf_filter_dict() (in module gnomad.utils.vcf) MatrixTableResource (class in gnomad.resources.resource_utils) median_impute_features() (in module gnomad.variant_qc.random_forest) merge_freq_arrays() (in module gnomad.utils.annotations) merge_histograms() (in module gnomad.utils.annotations) merge_sample_qc_expr() (in module gnomad.sample_qc.filtering) merge_stats_counters_expr() (in module gnomad.utils.gen_stats) missing_callstats_expr() (in module gnomad.utils.annotations) missing_struct_expr() (in module gnomad.utils.annotations) module gnomad.assessment.summary_stats gnomad.assessment.validity_checks gnomad.resources.config gnomad.resources.grch37.gnomad gnomad.resources.grch37.gnomad_ld gnomad.resources.grch37.reference_data gnomad.resources.grch38.gnomad gnomad.resources.grch38.reference_data gnomad.resources.import_resources gnomad.resources.resource_utils gnomad.sample_qc.ancestry gnomad.sample_qc.filtering gnomad.sample_qc.pipeline gnomad.sample_qc.platform gnomad.sample_qc.relatedness gnomad.sample_qc.sex gnomad.utils.annotations gnomad.utils.constraint gnomad.utils.file_utils gnomad.utils.filtering gnomad.utils.gen_stats gnomad.utils.intervals gnomad.utils.liftover gnomad.utils.parse gnomad.utils.plotting gnomad.utils.reference_genome gnomad.utils.release gnomad.utils.slack gnomad.utils.sparse_mt gnomad.utils.transcript_annotation gnomad.utils.vcf gnomad.utils.vep gnomad.variant_qc.evaluation gnomad.variant_qc.ld gnomad.variant_qc.pipeline gnomad.variant_qc.random_forest gnomad.variant_qc.training

mt() (gnomad.resources.resource_utils.GnomadPublicMatrixTableResource method) (gnomad.resources.resource_utils.MatrixTableResource method)

N

new_show() (in module gnomad.utils.plotting)

O

oe_aggregation_expr() (in module gnomad.utils.constraint)

oe_confidence_interval() (in module gnomad.utils.constraint)

P

pab_max_expr() (in module gnomad.utils.annotations) pair_plot() (in module gnomad.utils.plotting) PARENT_CHILD (in module gnomad.sample_qc.relatedness) parse_variant() (in module gnomad.utils.parse) path (gnomad.resources.resource_utils.BaseResource property) pc_project() (in module gnomad.sample_qc.ancestry) pedigree() (gnomad.resources.resource_utils.GnomadPublicPedigreeResource method) (gnomad.resources.resource_utils.PedigreeResource method) PedigreeResource (class in gnomad.resources.resource_utils) perform_tx_annotation_pipeline() (in module gnomad.utils.transcript_annotation) pext() (in module gnomad.resources.grch37.gnomad) (in module gnomad.resources.grch38.gnomad) plot_hail_file_metadata() (in module gnomad.utils.plotting) plot_hail_hist() (in module gnomad.utils.plotting)

plot_hail_hist_both() (in module gnomad.utils.plotting) plot_hail_hist_cumulative() (in module gnomad.utils.plotting) plot_multi_hail_hist() (in module gnomad.utils.plotting) pop_max_expr() (in module gnomad.utils.annotations) POPS (in module gnomad.resources.grch38.gnomad) POPS_TO_REMOVE_FOR_POPMAX (in module gnomad.resources.grch38.gnomad) POSSIBLE_REFS (in module gnomad.utils.vep) pprint_global_anns() (in module gnomad.assessment.validity_checks) pretty_print_runs() (in module gnomad.variant_qc.random_forest) process_consequences() (in module gnomad.utils.vep) project_max_expr() (in module gnomad.utils.annotations) public_pca_loadings() (in module gnomad.resources.grch37.gnomad) public_release() (in module gnomad.resources.grch37.gnomad) (in module gnomad.resources.grch38.gnomad)

Q

qual_hist_expr() (in module gnomad.utils.annotations)

R

read_list_data() (in module gnomad.utils.file_utils) region_flag_expr() (in module gnomad.utils.annotations) REGION_FLAG_FIELDS (in module gnomad.utils.vcf) REGISTRY_OF_OPEN_DATA_ON_AWS (gnomad.resources.config.GnomadPublicResourceSource attribute) rekey_new_reference() (in module gnomad.utils.vcf) release_vcf_path() (in module gnomad.resources.grch37.gnomad) (in module gnomad.resources.grch38.gnomad) remove_fields_from_constant() (in module gnomad.utils.filtering) repartition_for_join() (in module gnomad.utils.file_utils) REPRODUCTIVE_TISSUES (in module gnomad.utils.transcript_annotation)

resource_class (gnomad.resources.resource_utils.BaseVersionedResource attribute) (gnomad.resources.resource_utils.VersionedBlockMatrixResource attribute) (gnomad.resources.resource_utils.VersionedMatrixTableResource attribute) (gnomad.resources.resource_utils.VersionedPedigreeResource attribute) (gnomad.resources.resource_utils.VersionedTableResource attribute) (gnomad.resources.resource_utils.VersionedVariantDatasetResource attribute) ResourceNotAvailable RF_FIELDS (in module gnomad.utils.vcf) run_pca_with_relateds() (in module gnomad.sample_qc.ancestry) run_platform_pca() (in module gnomad.sample_qc.platform) run_rf_test() (in module gnomad.variant_qc.random_forest)

S

sample_training_examples() (in module gnomad.variant_qc.training) save_model() (in module gnomad.variant_qc.random_forest) scale_file_sizes() (in module gnomad.utils.plotting) score_bin_agg() (in module gnomad.variant_qc.pipeline) SECOND_DEGREE_RELATIVES (in module gnomad.sample_qc.relatedness) select_primitives_from_ht() (in module gnomad.utils.file_utils) send_file() (gnomad.utils.slack.SlackClient method) send_message() (gnomad.utils.slack.SlackClient method) set_female_y_metrics_to_na() (in module gnomad.utils.vcf) set_female_y_metrics_to_na_expr() (in module gnomad.utils.annotations) set_font_size() (in module gnomad.utils.plotting) SEXES (in module gnomad.resources.grch38.gnomad) (in module gnomad.utils.vcf) SIBLINGS (in module gnomad.sample_qc.relatedness) SITE_FIELDS (in module gnomad.utils.vcf)

slack_notifications() (in module gnomad.utils.slack) SlackClient (class in gnomad.utils.slack) sor_from_sb() (in module gnomad.utils.annotations) sort_intervals() (in module gnomad.utils.intervals) SORT_ORDER (in module gnomad.utils.vcf) SPARSE_ENTRIES (in module gnomad.utils.vcf) split_info_annotation() (in module gnomad.utils.sparse_mt) split_lowqual_annotation() (in module gnomad.utils.sparse_mt) split_vds_by_strata() (in module gnomad.utils.filtering) subset_samples_and_variants() (in module gnomad.utils.filtering) SUBSETS (in module gnomad.resources.grch38.gnomad) sum_group_callstats() (in module gnomad.assessment.validity_checks) summarize_transcript_expression() (in module gnomad.utils.transcript_annotation) summarize_variant_filters() (in module gnomad.assessment.validity_checks) summarize_variants() (in module gnomad.assessment.validity_checks)

T

TableResource (class in gnomad.resources.resource_utils) test_model() (in module gnomad.variant_qc.random_forest) TGP_POP_NAMES (in module gnomad.resources.grch38.gnomad) TGP_POPS (in module gnomad.resources.grch38.gnomad) tissue_expression_ht_to_array() (in module gnomad.utils.transcript_annotation) to_phred() (in module gnomad.utils.gen_stats) train_rf() (in module gnomad.variant_qc.random_forest)

train_rf_model() (in module gnomad.variant_qc.pipeline) transform_grch37_methylation() (in module gnomad.resources.grch37.reference_data) transform_grch38_methylation() (in module gnomad.resources.grch38.reference_data) transform_methylation_level() (in module gnomad.utils.constraint) trimer_from_heptamer() (in module gnomad.utils.constraint) tx_aggregate_variants() (in module gnomad.utils.transcript_annotation) tx_annotate_variants() (in module gnomad.utils.transcript_annotation) tx_filter_variants_by_csqs() (in module gnomad.utils.transcript_annotation)

U

union_intervals() (in module gnomad.utils.intervals) unphase_call_expr() (in module gnomad.utils.annotations)

UNRELATED (in module gnomad.sample_qc.relatedness) update_structured_annotations() (in module gnomad.utils.annotations)

V

validate_release_t() (in module gnomad.assessment.validity_checks) VariantDatasetResource (class in gnomad.resources.resource_utils) vcf_field_check() (in module gnomad.assessment.validity_checks) vds() (gnomad.resources.resource_utils.VariantDatasetResource method) VEP_CONFIG_PATH (in module gnomad.utils.vep) VEP_CSQ_FIELDS (in module gnomad.utils.vep) VEP_CSQ_HEADER (in module gnomad.utils.vep) vep_or_lookup_vep() (in module gnomad.utils.vep)

vep_struct_to_csq() (in module gnomad.utils.vep) VersionedBlockMatrixResource (class in gnomad.resources.resource_utils) VersionedMatrixTableResource (class in gnomad.resources.resource_utils) VersionedPedigreeResource (class in gnomad.resources.resource_utils) VersionedTableResource (class in gnomad.resources.resource_utils) VersionedVariantDatasetResource (class in gnomad.resources.resource_utils) versions (gnomad.resources.resource_utils.BaseVersionedResource attribute) VQSR_FIELDS (in module gnomad.utils.vcf) VRS_FIELDS_DICT (in module gnomad.utils.vcf)

W

write_temp_gcs() (in module gnomad.utils.file_utils)