gnomad.utils

• annotations
  • annotate_with_ht()
  • grpmax_expr()
  • project_max_expr()
  • faf_expr()
  • gen_anc_faf_max_expr()
  • qual_hist_expr()
  • age_hists_expr()
  • get_lowqual_expr()
  • get_annotations_hists()
  • create_frequency_bins_expr()
  • annotate_and_index_source_mt_for_sex_ploidy()
  • get_is_haploid_expr()
  • get_gq_dp_adj_expr()
  • get_het_ab_adj_expr()
  • get_adj_expr()
  • annotate_adj()
  • add_variant_type()
  • annotate_allele_info()
  • annotation_type_is_numeric()
  • annotation_type_in_vcf_info()
  • bi_allelic_site_inbreeding_expr()
  • fs_from_sb()
  • sor_from_sb()
  • pab_max_expr()
  • bi_allelic_expr()
  • unphase_call_expr()
  • region_flag_expr()
  • missing_callstats_expr()
  • set_xx_y_metrics_to_na_expr()
  • hemi_expr()
  • merge_array_expressions()
  • merge_freq_arrays()
  • merge_histograms()
  • annotate_freq()
  • annotate_downsamplings()
  • build_freq_stratification_list()
  • generate_freq_group_membership_array()
  • compute_freq_by_strata()
  • agg_by_strata()
  • update_structured_annotations()
  • fill_missing_key_combinations()
  • missing_struct_expr()
  • add_gks_vrs()
  • add_gks_va()
  • get_copy_state_by_sex()
• constraint
  • COVERAGE_CUTOFF
  • get_mu_annotation_expr()
  • annotate_with_mu()
  • count_variants_by_group()
  • get_downsampling_freq_indices()
  • downsampling_counts_expr()
  • explode_downsamplings_oe()
  • annotate_mutation_type()
  • trimer_from_heptamer()
  • collapse_strand()
  • transform_methylation_level()
  • assemble_constraint_context_ht()
  • build_models()
  • build_plateau_models()
  • build_coverage_model()
  • get_all_gen_anc_lengths()
  • get_constraint_grouping_expr()
  • annotate_exploded_vep_for_constraint_groupings()
  • compute_expected_variants()
  • oe_aggregation_expr()
  • compute_pli()
  • oe_confidence_interval()
  • calculate_raw_z_score()
  • get_constraint_flags()
  • calculate_raw_z_score_sd()
  • add_gencode_transcript_annotations()
• file_utils
  • file_exists()
  • check_file_exists_raise_error()
  • write_temp_gcs()
  • select_primitives_from_ht()
  • get_file_stats()
  • read_list_data()
  • repartition_for_join()
  • create_vds()
• filtering
  • filter_to_adj()
  • filter_by_frequency()
  • combine_functions()
  • low_conf_regions_expr()
  • filter_low_conf_regions()
  • filter_to_autosomes()
  • add_filters_expr()
  • subset_samples_and_variants()
  • filter_to_clinvar_pathogenic()
  • filter_gencode_ht()
  • filter_by_intervals()
  • filter_by_gencode_intervals()
  • filter_to_gencode_cds()
  • remove_fields_from_constant()
  • filter_x_nonpar()
  • filter_y_nonpar()
  • filter_by_numeric_expr_range()
  • filter_for_mu()
  • split_vds_by_strata()
  • filter_arrays_by_meta()
• gen_stats
  • to_phred()
  • from_phred()
  • get_median_and_mad_expr()
  • merge_stats_counters_expr()
• intervals
  • sort_intervals()
  • union_intervals()
  • interval_length()
  • pad_intervals()
• liftover
  • GRCH37_to_GRCH38_CHAIN
  • GRCH38_TO_GRCH37_CHAIN
  • get_liftover_genome()
  • liftover_expr()
  • default_lift_data()
  • liftover_using_gnomad_map()
• parse
  • parse_variant()
  • parse_locus_intervals()
• plotting
  • new_show()
  • plot_hail_hist()
  • plot_multi_hail_hist()
  • plot_hail_hist_cumulative()
  • plot_hail_hist_both()
  • set_font_size()
  • linear_and_log_tabs()
  • plot_hail_file_metadata()
  • scale_file_sizes()
  • get_rows_data()
  • pair_plot()
• reference_genome
  • get_reference_ht()
  • add_reference_sequence()
  • get_reference_genome()
• release
  • make_faf_index_dict()
  • make_freq_index_dict()
  • make_freq_index_dict_from_meta()
• slack
  • SlackClient
  • slack_notifications()
• sparse_mt
  • compute_last_ref_block_end()
  • densify_sites()
  • get_as_info_expr()
  • get_site_info_expr()
  • default_compute_info()
  • split_info_annotation()
  • split_lowqual_annotation()
  • impute_sex_ploidy()
  • densify_all_reference_sites()
  • compute_stats_per_ref_site()
  • get_coverage_agg_func()
  • compute_coverage_stats()
  • get_allele_number_agg_func()
  • compute_allele_number_per_ref_site()
  • filter_ref_blocks()
• transcript_annotation
  • REPRODUCTIVE_TISSUES
  • CELL_LINES
  • get_tissues_to_exclude()
  • summarize_transcript_expression()
  • get_expression_proportion()
  • filter_expression_ht_by_tissues()
  • tissue_expression_ht_to_array()
  • tx_filter_variants_by_csqs()
  • tx_annotate_variants()
  • tx_aggregate_variants()
  • perform_tx_annotation_pipeline()
  • clean_tissue_name_for_browser()
  • create_tx_annotation_by_region()
• vcf
  • SORT_ORDER
  • GROUPS
  • HISTS
  • FAF_GEN_ANC_GROUPS
  • SEXES
  • AS_FIELDS
  • SITE_FIELDS
  • ALLELE_TYPE_FIELDS
  • REGION_FLAG_FIELDS
  • JOINT_REGION_FLAG_FIELDS
  • RF_FIELDS
  • AS_VQSR_FIELDS
  • VQSR_FIELDS
  • INFO_DICT
  • IN_SILICO_ANNOTATIONS_INFO_DICT
  • VRS_FIELDS_DICT
  • ENTRIES
  • SPARSE_ENTRIES
  • FORMAT_DICT
  • adjust_vcf_incompatible_types()
  • make_label_combos()
  • index_globals()
  • make_combo_header_text()
  • create_label_groups()
  • make_info_dict()
  • add_as_info_dict()
  • make_vcf_filter_dict()
  • make_hist_bin_edges_expr()
  • make_hist_dict()
  • set_xx_y_metrics_to_na()
  • build_vcf_export_reference()
  • rekey_new_reference()
• vep
  • CURRENT_VEP_VERSION
  • CSQ_CODING
  • CSQ_SPLICE
  • POSSIBLE_REFS
  • VEP_CONFIG_PATH
  • VEP_CSQ_FIELDS
  • VEP_CSQ_HEADER
  • LOFTEE_LABELS
  • LOF_CSQ_SET
  • get_vep_help()
  • get_vep_context()
  • vep_or_lookup_vep()
  • get_most_severe_consequence_expr()
  • add_most_severe_consequence_to_consequence()
  • process_consequences()
  • filter_vep_to_canonical_transcripts()
  • filter_vep_to_mane_select_transcripts()
  • filter_vep_to_synonymous_variants()
  • filter_vep_to_gene_list()
  • vep_struct_to_csq()
  • get_most_severe_consequence_for_summary()
  • filter_vep_transcript_csqs()
  • filter_vep_transcript_csqs_expr()
  • add_most_severe_csq_to_tc_within_vep_root()
  • explode_by_vep_annotation()
  • get_loftee_end_trunc_filter_expr()
  • update_loftee_end_trunc_filter()