Index

A

add_all_sites_an_and_qual_hists() (in module gnomad_qc.v4.create_release.create_combined_faf_release_ht) add_annotations() (in module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht) add_exomes_interval_annotations() (in module gnomad_qc.v4.annotations.compute_coverage) add_meta() (in module gnomad_qc.v4.resources.basics) add_model_to_run_list() (in module gnomad_qc.v4.variant_qc.random_forest) add_project_prefix_to_sample_collisions() (in module gnomad_qc.v5.resources.basics) add_updated_sample_qc_annotations() (in module gnomad_qc.v4.annotations.generate_freq_genomes) add_variant_qc (gnomad_qc.v4.subset.ProcessingConfig attribute) adjust_all_sites_an_and_hists() (in module gnomad_qc.v4.annotations.fix_freq_an) adjust_interval_padding() (in module gnomad_qc.v4.annotations.compute_coverage) adjust_per_site_an_and_hists_for_frequency() (in module gnomad_qc.v4.annotations.fix_freq_an) AGE_HISTS (in module gnomad_qc.v4.annotations.generate_freq) aggregate_and_annotate_de_novos() (in module gnomad_qc.v4.create_release.create_de_novo_release) ALL_FREQ_ROW_FIELDS (in module gnomad_qc.v4.annotations.generate_freq) ALLELE_TYPE_FIELDS (in module gnomad_qc.v4.variant_qc.final_filter_genomes) ancestry_pca_eigenvalues() (in module gnomad_qc.v4.resources.sample_qc) ancestry_pca_loadings() (in module gnomad_qc.v4.resources.sample_qc) ancestry_pca_scores() (in module gnomad_qc.v4.resources.sample_qc) annotate_freq_index_dict() (in module gnomad_qc.v4.annotations.generate_freq) annotate_interval_qc_filter() (in module gnomad_qc.v4.sample_qc.interval_qc)

annotate_per_sample_stat_combinations() (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) annotate_relatedness_filters() (in module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht) annotate_relationships() (in module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht) annotate_sex_karyotype_from_ploidy_cutoffs() (in module gnomad_qc.v4.sample_qc.sex_inference) annotate_v3_subsets_sample_count() (in module gnomad_qc.v4.annotations.generate_freq_genomes) annotation_hists_params_path() (in module gnomad_qc.v4.resources.release) aou_acaf_mt (in module gnomad_qc.v5.resources.basics) aou_exome_mt (in module gnomad_qc.v5.resources.basics) append_to_vcf_header_path() (in module gnomad_qc.v4.resources.release) apply_filter() (in module gnomad_qc.v4.sample_qc.outlier_filtering) apply_min_rep_logic() (in module gnomad_qc.v4.subset) apply_n_singleton_filter_to_r_ti_tv_singleton() (in module gnomad_qc.v4.sample_qc.outlier_filtering) apply_nearest_neighbor_filtering_method() (in module gnomad_qc.v4.sample_qc.outlier_filtering) apply_recalibration() (in module gnomad_qc.v4.variant_qc.vqsr) apply_regressed_filtering_method() (in module gnomad_qc.v4.sample_qc.outlier_filtering) apply_split_multi_logic() (in module gnomad_qc.v4.subset) apply_stratified_filtering_method() (in module gnomad_qc.v4.sample_qc.outlier_filtering) apply_variant_qc_annotations() (in module gnomad_qc.v4.subset) assign_pop_with_per_pop_probs() (in module gnomad_qc.v4.sample_qc.assign_ancestry) assign_pops() (in module gnomad_qc.v4.sample_qc.assign_ancestry)

C

calculate_callstats_for_selected_samples() (in module gnomad_qc.v4.annotations.generate_freq_genomes) calling_intervals() (in module gnomad_qc.v4.resources.basics) check_globals_for_retired_terms() (in module gnomad_qc.v4.create_release.validate_and_export_vcf) check_missingness() (in module gnomad_qc.v5.data_ingestion.federated_validity_checks) check_subset_ht() (in module gnomad_qc.v4.subset) CHR_LIST (in module gnomad_qc.v4.create_release.create_combined_faf_release_ht) combine_autosome_and_sex_chr_stats() (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) combine_freq_hts() (in module gnomad_qc.v4.annotations.generate_freq) COMMON_FILTER_COMBOS (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) COMMON_FILTERS (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) compute_agg_sample_stats() (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) compute_allele_number_per_ref_site() (in module gnomad_qc.v4.annotations.fix_freq_an) compute_an_and_hists_het_fail_adj_ab() (in module gnomad_qc.v4.annotations.fix_freq_an) compute_an_and_qual_hists_per_ref_site() (in module gnomad_qc.v4.annotations.compute_coverage) compute_an_by_group_membership() (in module gnomad_qc.v4.annotations.generate_freq_genomes) compute_hard_filters() (in module gnomad_qc.v4.sample_qc.hard_filters) compute_ibd_on_cuking_pair_subset() (in module gnomad_qc.v4.sample_qc.relatedness) compute_inbreeding_coeff() (in module gnomad_qc.v4.annotations.generate_freq) compute_interval_qc() (in module gnomad_qc.v4.sample_qc.interval_qc) compute_precision_recall() (in module gnomad_qc.v4.sample_qc.assign_ancestry) compute_rank_ht() (in module gnomad_qc.v4.sample_qc.relatedness) compute_sample_qc() (in module gnomad_qc.v4.sample_qc.hard_filters) compute_sex_ploidy() (in module gnomad_qc.v4.sample_qc.sex_inference) concatenate_annotations() (in module gnomad_qc.v4.annotations.generate_freq_genomes) consent_samples_to_drop (in module gnomad_qc.v5.resources.meta) correct_as_annotations() (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations)

correct_for_high_ab_hets() (in module gnomad_qc.v4.annotations.generate_freq) create_aggregated_bin_ht() (in module gnomad_qc.v4.variant_qc.evaluation) create_bin_ht() (in module gnomad_qc.v4.variant_qc.evaluation) create_cadd_grch38_ht() (in module gnomad_qc.v4.annotations.insilico_predictors) create_dense_trio_mt() (in module gnomad_qc.v4.sample_qc.identify_trios) create_filtered_dense_mt() (in module gnomad_qc.v4.sample_qc.generate_qc_mt) create_final_combined_faf_release() (in module gnomad_qc.v4.create_release.create_combined_faf_release_ht) create_final_freq_ht() (in module gnomad_qc.v4.annotations.generate_freq) create_finalized_outlier_filter_ht() (in module gnomad_qc.v4.sample_qc.outlier_filtering) create_frequency_bins_expr_inbreeding() (in module gnomad_qc.v4.create_release.make_var_annot_hists) create_intermediate_mt_for_sample_counts() (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) create_logtest_ht() (in module gnomad_qc.v5.data_ingestion.federated_validity_checks) create_pangolin_grch38_ht() (in module gnomad_qc.v4.annotations.insilico_predictors) create_per_sample_counts_from_intermediate_ht() (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) create_per_sample_counts_ht() (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) create_phylop_grch38_ht() (in module gnomad_qc.v4.annotations.insilico_predictors) create_revel_grch38_ht() (in module gnomad_qc.v4.annotations.insilico_predictors) create_spliceai_grch38_ht() (in module gnomad_qc.v4.annotations.insilico_predictors) create_variant_qc_annotation_ht() (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations) custom_filters_select() (in module gnomad_qc.v4.create_release.create_release_sites_ht) custom_filters_select_globals() (in module gnomad_qc.v4.create_release.create_release_sites_ht) custom_freq_select() (in module gnomad_qc.v4.create_release.create_release_sites_ht) custom_in_silico_select() (in module gnomad_qc.v4.create_release.create_release_sites_ht) custom_info_select() (in module gnomad_qc.v4.create_release.create_release_sites_ht) custom_joint_faf_select() (in module gnomad_qc.v4.create_release.create_release_sites_ht) custom_region_flags_select() (in module gnomad_qc.v4.create_release.create_release_sites_ht) custom_vep_select() (in module gnomad_qc.v4.create_release.create_release_sites_ht)

D

data_type (gnomad_qc.v4.subset.ProcessingConfig attribute) dense_trio_mt() (in module gnomad_qc.v4.resources.sample_qc) densify_and_prep_vds_for_freq() (in module gnomad_qc.v4.annotations.generate_freq)

determine_fstat_sites() (in module gnomad_qc.v4.sample_qc.sex_inference) drop_gatk_groupings() (in module gnomad_qc.v4.annotations.fix_freq_an) drop_v3_subsets() (in module gnomad_qc.v4.create_release.create_release_sites_ht) duplicates() (in module gnomad_qc.v4.resources.sample_qc)

E

export_meta (gnomad_qc.v4.subset.ProcessingConfig attribute)

extract_as_pls() (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations) extract_freq_info() (in module gnomad_qc.v4.create_release.create_combined_faf_release_ht)

F

failing_metrics_samples (in module gnomad_qc.v5.resources.meta) families_to_trios() (in module gnomad_qc.v4.sample_qc.identify_trios) filter_freq_arrays() (in module gnomad_qc.v4.annotations.generate_freq_genomes) filter_freq_arrays_for_non_ukb_subset() (in module gnomad_qc.v4.annotations.generate_freq) filter_gene_to_test() (in module gnomad_qc.v4.create_release.create_combined_faf_release_ht) filter_liftover_to_false_dups() (in module gnomad_qc.v4.create_release.create_false_dup_liftover) filter_ped() (in module gnomad_qc.v4.sample_qc.identify_trios) filter_ped_to_same_platform() (in module gnomad_qc.v4.sample_qc.identify_trios) filter_relatedness_ht() (in module gnomad_qc.v4.sample_qc.identify_trios) filter_to_pass_only() (in module gnomad_qc.v4.subset) filter_to_test() (in module gnomad_qc.analyses.compute_pext) (in module gnomad_qc.v4.annotations.generate_freq_genomes) (in module gnomad_qc.v4.create_release.validate_and_export_vcf) (in module gnomad_qc.v4.sample_qc.interval_qc)

final_filter() (in module gnomad_qc.v4.resources.variant_qc) FINAL_FILTER_FIELDS (in module gnomad_qc.v4.variant_qc.final_filter) (in module gnomad_qc.v4.variant_qc.final_filter_genomes) finalize_relatedness_ht() (in module gnomad_qc.v4.sample_qc.relatedness) finalize_v4_genomes_callstats() (in module gnomad_qc.v4.annotations.generate_freq_genomes) finalized_outlier_filtering() (in module gnomad_qc.v4.resources.sample_qc) (in module gnomad_qc.v5.resources.sample_qc) format_validated_ht_for_export() (in module gnomad_qc.v4.create_release.validate_and_export_vcf) format_vcf_info_fields() (in module gnomad_qc.v4.subset) FREQ_GLOBAL_FIELDS (in module gnomad_qc.v4.annotations.generate_freq) FREQ_GLOBALS (in module gnomad_qc.v4.annotations.generate_freq_genomes) FREQ_HIGH_AB_HET_ROW_FIELDS (in module gnomad_qc.v4.annotations.generate_freq) FREQ_ROW_FIELDS (in module gnomad_qc.v4.annotations.generate_freq) from_args() (gnomad_qc.v4.subset.ProcessingConfig class method)

G

gather_tranches() (in module gnomad_qc.v4.variant_qc.vqsr) gather_vcfs() (in module gnomad_qc.v4.variant_qc.vqsr) gen_anc_rf_path() (in module gnomad_qc.v5.resources.sample_qc) generate_faf_grpmax() (in module gnomad_qc.v4.annotations.generate_freq) generate_final_filter_ht() (in module gnomad_qc.v4.variant_qc.final_filter) generate_freq_ht() (in module gnomad_qc.v4.annotations.generate_freq) generate_qc_meta_ht() (in module gnomad_qc.v4.sample_qc.generate_qc_mt) generate_qc_mt() (in module gnomad_qc.v4.sample_qc.generate_qc_mt) generate_sex_chr_interval_coverage_mt() (in module gnomad_qc.v4.sample_qc.interval_qc) generate_v4_genomes_callstats() (in module gnomad_qc.v4.annotations.generate_freq_genomes) genetic_ancestry_pca_eigenvalues() (in module gnomad_qc.v5.resources.sample_qc) genetic_ancestry_pca_loadings() (in module gnomad_qc.v5.resources.sample_qc) genetic_ancestry_pca_scores() (in module gnomad_qc.v5.resources.sample_qc) get_age_distribution() (in module gnomad_qc.v4.annotations.generate_freq_genomes) get_all_sites_an_and_qual_hists() (in module gnomad_qc.v4.resources.annotations) get_all_sites_nonref_adjustment() (in module gnomad_qc.v4.annotations.fix_freq_an) get_aou_failing_genomic_metrics_samples() (in module gnomad_qc.v5.resources.basics) get_aou_mt_union() (in module gnomad_qc.v5.resources.sample_qc) get_aou_vds() (in module gnomad_qc.v5.resources.basics) get_binned_concordance() (in module gnomad_qc.v4.resources.variant_qc) get_callset_truth_data() (in module gnomad_qc.v4.resources.variant_qc) get_capture_filter_exprs() (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) get_checkpoint_path() (in module gnomad_qc.v4.resources.basics) (in module gnomad_qc.v5.resources.basics) get_combine_faf_resources() (in module gnomad_qc.v4.create_release.create_combined_faf_release_ht) get_combined_frequency() (in module gnomad_qc.v4.resources.annotations) get_config() (in module gnomad_qc.v4.create_release.create_release_sites_ht) get_coverage_resources() (in module gnomad_qc.v4.annotations.compute_coverage) get_cuking_input_path() (in module gnomad_qc.v4.resources.sample_qc) (in module gnomad_qc.v5.resources.sample_qc) get_cuking_output_path() (in module gnomad_qc.v4.resources.sample_qc) (in module gnomad_qc.v5.resources.sample_qc) get_downsampling() (in module gnomad_qc.v4.resources.annotations) get_downsampling_ht() (in module gnomad_qc.v4.annotations.generate_freq) get_downsamplings_fields() (in module gnomad_qc.v4.create_release.validate_and_export_vcf) get_evaluation_resources() (in module gnomad_qc.v4.variant_qc.evaluation) get_exomes_group_membership_ht() (in module gnomad_qc.v4.annotations.compute_coverage) get_export_resources() (in module gnomad_qc.v4.create_release.validate_and_export_vcf) get_false_dup_genes_path() (in module gnomad_qc.v4.resources.release) get_final_ht_fields() (in module gnomad_qc.v4.create_release.create_release_sites_ht) get_final_variant_qc_resources() (in module gnomad_qc.v4.variant_qc.final_filter) (in module gnomad_qc.v4.variant_qc.final_filter_genomes) get_freq() (in module gnomad_qc.v4.resources.annotations) get_freq_array_readme() (in module gnomad_qc.v4.resources.release) get_freq_comparison() (in module gnomad_qc.v4.resources.annotations) get_freq_resources() (in module gnomad_qc.v4.annotations.generate_freq) get_gen_anc_ht() (in module gnomad_qc.v5.resources.sample_qc) get_gen_anc_pr_ht() (in module gnomad_qc.v5.resources.sample_qc) get_genomes_group_membership_ht() (in module gnomad_qc.v4.annotations.compute_coverage) get_gnomad_datasets() (in module gnomad_qc.v4.subset) get_gnomad_v4_genomes_vds() (in module gnomad_qc.v4.resources.basics) get_gnomad_v4_vds() (in module gnomad_qc.v4.resources.basics) get_group_membership_ht_for_an() (in module gnomad_qc.v4.annotations.generate_freq_genomes) get_hard_filter_metric_ht() (in module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht) get_hard_filters_ht() (in module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht) get_hgdp_tgp_callstats_for_selected_samples() (in module gnomad_qc.v4.annotations.generate_freq_genomes) get_hgdp_tgp_related_to_nonsubset() (in module gnomad_qc.v4.annotations.generate_freq_genomes) get_hgdp_tgp_v4_exome_duplicates() (in module gnomad_qc.v4.annotations.generate_freq_genomes) get_high_qual_cutoff_dict() (in module gnomad_qc.v4.sample_qc.interval_qc) get_histograms() (in module gnomad_qc.v4.annotations.generate_freq_genomes) get_ht() (in module gnomad_qc.v4.create_release.create_release_sites_ht) get_info() (in module gnomad_qc.v4.resources.annotations) get_info_ht_for_vcf_export() (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations) get_insilico_predictors() (in module gnomad_qc.v4.resources.annotations) get_interval_qc_pass() (in module gnomad_qc.v4.sample_qc.interval_qc) get_joint_filters() (in module gnomad_qc.v4.create_release.validate_and_export_vcf) get_joint_freq_and_faf() (in module gnomad_qc.v4.create_release.create_combined_faf_release_ht) get_joint_qc() (in module gnomad_qc.v4.resources.sample_qc) (in module gnomad_qc.v5.resources.sample_qc) get_logging_path() (in module gnomad_qc.v4.resources.basics) (in module gnomad_qc.v5.resources.basics) get_most_likely_pop_expr() (in module gnomad_qc.v4.sample_qc.assign_ancestry) get_outlier_detection_sample_qc() (in module gnomad_qc.v5.resources.sample_qc) get_outlier_filtering_resources() (in module gnomad_qc.v4.sample_qc.outlier_filtering) get_per_sample_counts() (in module gnomad_qc.v4.resources.assessment) get_pext() (in module gnomad_qc.analyses.resources) get_pipeline_resources() (in module gnomad_qc.analyses.compute_pext) (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) get_ploidy_cutoff_json_path() (in module gnomad_qc.v4.resources.sample_qc) get_pop_diff_v3_vds_group_membership() (in module gnomad_qc.v4.annotations.generate_freq_genomes) get_pop_ht() (in module gnomad_qc.v4.resources.sample_qc) get_pop_pr_ht() (in module gnomad_qc.v4.resources.sample_qc) get_predetermined_qc() (in module gnomad_qc.v4.resources.sample_qc) get_project_meta() (in module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht) get_reformatted_info_fields() (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations) get_relatedness_dict_ht() (in module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht) get_relatedness_resources() (in module gnomad_qc.v4.sample_qc.relatedness) get_relationship_filter_expr() (in module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht) get_releasable_de_novo_calls_ht() (in module gnomad_qc.v4.create_release.create_de_novo_release) get_revel_for_unmatched_transcripts() (in module gnomad_qc.v4.annotations.insilico_predictors) get_rf_model_path() (in module gnomad_qc.v4.resources.variant_qc) get_rf_run_path() (in module gnomad_qc.v4.resources.variant_qc) get_rf_training() (in module gnomad_qc.v4.resources.variant_qc) get_sample_filter_ht() (in module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht) get_sample_qc() (in module gnomad_qc.v4.resources.sample_qc) (in module gnomad_qc.v5.resources.sample_qc) get_sample_qc_field_def_json_path() (in module gnomad_qc.v4.resources.sample_qc) get_sample_qc_ht() (in module gnomad_qc.v4.sample_qc.outlier_filtering) get_sample_qc_meta_ht() (in module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht) get_sample_qc_root() (in module gnomad_qc.v4.resources.sample_qc) (in module gnomad_qc.v5.resources.sample_qc) get_samples_to_exclude() (in module gnomad_qc.v5.resources.basics) get_score_bins() (in module gnomad_qc.v4.resources.variant_qc) get_select_fields() (in module gnomad_qc.v4.create_release.create_release_sites_ht) get_select_global_fields() (in module gnomad_qc.v4.create_release.create_release_sites_ht) get_sex_imputation_ht() (in module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht) get_sib_stats() (in module gnomad_qc.v4.resources.annotations) get_sift_polyphen_from_vep() (in module gnomad_qc.v4.annotations.insilico_predictors) get_split_vds() (in module gnomad_qc.v4.resources.annotations) get_sub_hist_expr() (in module gnomad_qc.v4.annotations.fix_freq_an) get_subset_ht() (in module gnomad_qc.v4.subset) get_summary_stats_filter_groups_ht() (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) get_summary_stats_filtering_groups() (in module gnomad_qc.v4.resources.assessment) get_table_kind() (in module gnomad_qc.v5.data_ingestion.federated_validity_checks) get_tp_ht_for_vcf_export() (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations) get_trio_resources() (in module gnomad_qc.v4.sample_qc.identify_trios) get_trio_stats() (in module gnomad_qc.v4.resources.annotations)

get_true_positive_vcf_path() (in module gnomad_qc.v4.resources.annotations) get_updated_release_samples() (in module gnomad_qc.v4.annotations.generate_freq_genomes) get_v4_genomes_release_resources() (in module gnomad_qc.v4.annotations.generate_freq_genomes) get_variant_qc_annotation_resources() (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations) get_variant_qc_annotations() (in module gnomad_qc.v4.resources.annotations) get_variant_qc_resources() (in module gnomad_qc.v4.variant_qc.random_forest) get_variant_qc_result() (in module gnomad_qc.v4.resources.variant_qc) get_vds_for_freq() (in module gnomad_qc.v4.annotations.generate_freq) get_vep() (in module gnomad_qc.v4.resources.annotations) get_vrs() (in module gnomad_qc.v4.resources.annotations) gnomad_qc.analyses.compute_pext module gnomad_qc.analyses.resources module gnomad_qc.v4.annotations.compute_coverage module gnomad_qc.v4.annotations.fix_freq_an module gnomad_qc.v4.annotations.generate_freq module gnomad_qc.v4.annotations.generate_freq_genomes module gnomad_qc.v4.annotations.generate_variant_qc_annotations module gnomad_qc.v4.annotations.insilico_predictors module gnomad_qc.v4.annotations.vep_context_ht module gnomad_qc.v4.annotations.vrs_annotation_batch module gnomad_qc.v4.assessment.calculate_per_sample_stats module gnomad_qc.v4.assessment.summary_stats module gnomad_qc.v4.create_release.create_combined_faf_release_ht module gnomad_qc.v4.create_release.create_de_novo_release module gnomad_qc.v4.create_release.create_false_dup_liftover module gnomad_qc.v4.create_release.create_release_sites_ht module gnomad_qc.v4.create_release.create_release_utils module gnomad_qc.v4.create_release.make_var_annot_hists module gnomad_qc.v4.create_release.validate_and_export_vcf module gnomad_qc.v4.resources.annotations module gnomad_qc.v4.resources.assessment module gnomad_qc.v4.resources.basics module gnomad_qc.v4.resources.constants module gnomad_qc.v4.resources.meta module gnomad_qc.v4.resources.release module gnomad_qc.v4.resources.sample_qc module gnomad_qc.v4.resources.variant_qc module gnomad_qc.v4.sample_qc.assign_ancestry module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht_genomes module gnomad_qc.v4.sample_qc.generate_qc_mt module gnomad_qc.v4.sample_qc.hard_filters module gnomad_qc.v4.sample_qc.identify_trios module gnomad_qc.v4.sample_qc.interval_qc module gnomad_qc.v4.sample_qc.outlier_filtering module gnomad_qc.v4.sample_qc.platform_inference module gnomad_qc.v4.sample_qc.relatedness module gnomad_qc.v4.sample_qc.sex_inference module gnomad_qc.v4.subset module gnomad_qc.v4.variant_qc.evaluation module gnomad_qc.v4.variant_qc.final_filter module gnomad_qc.v4.variant_qc.final_filter_genomes module gnomad_qc.v4.variant_qc.import_variant_qc_vcf module gnomad_qc.v4.variant_qc.random_forest module gnomad_qc.v4.variant_qc.vqsr module gnomad_qc.v5.configs.validity_inputs_schema module gnomad_qc.v5.data_ingestion.create_vds module gnomad_qc.v5.data_ingestion.federated_validity_checks module gnomad_qc.v5.data_ingestion.field_md_to_html module gnomad_qc.v5.resources.basics module gnomad_qc.v5.resources.constants module gnomad_qc.v5.resources.meta module gnomad_qc.v5.resources.rwb_utils module gnomad_qc.v5.resources.sample_qc module

H

hail_type_from_string() (in module gnomad_qc.v5.data_ingestion.federated_validity_checks)

hgdp_tgp_updated_callstats() (in module gnomad_qc.v4.resources.annotations) high_ab_het() (in module gnomad_qc.v4.annotations.generate_freq)

I

ibd() (in module gnomad_qc.v4.resources.sample_qc) IF_FEATURES (in module gnomad_qc.v4.variant_qc.final_filter) import_updated_annotations() (in module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht_genomes) import_variant_qc_vcf() (in module gnomad_qc.v4.variant_qc.import_variant_qc_vcf) included_datasets_json_path() (in module gnomad_qc.v4.resources.release) indels_variant_recalibrator() (in module gnomad_qc.v4.variant_qc.vqsr) indels_variant_recalibrator_create_model() (in module gnomad_qc.v4.variant_qc.vqsr) infer_per_pop_min_rf_probs() (in module gnomad_qc.v4.sample_qc.assign_ancestry)

infer_sex_karyotype_from_ploidy() (in module gnomad_qc.v4.sample_qc.sex_inference) INFO_FEATURES (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations) INFO_METHODS (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations) info_vcf_path() (in module gnomad_qc.v4.resources.annotations) init_job() (in module gnomad_qc.v4.annotations.vrs_annotation_batch) init_job_with_gcloud() (in module gnomad_qc.v4.annotations.vrs_annotation_batch) interval_qc_pass() (in module gnomad_qc.v4.resources.sample_qc) is_concrete_type() (in module gnomad_qc.v5.data_ingestion.federated_validity_checks)

J

JOIN_FREQS (in module gnomad_qc.v4.annotations.generate_freq_genomes)

join_hts() (in module gnomad_qc.v4.create_release.create_release_sites_ht) join_release_ht_with_subsets() (in module gnomad_qc.v4.annotations.generate_freq_genomes)

K

keep_data_paths (gnomad_qc.v4.subset.ProcessingConfig attribute)

L

load_mt_for_sample_counts() (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) load_platform_ht() (in module gnomad_qc.v4.sample_qc.sex_inference) LOF_FILTER_COMBOS (in module gnomad_qc.v4.assessment.calculate_per_sample_stats)

LOF_FILTERS_FOR_COMBO (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) LOG10_ANNOTATIONS (in module gnomad_qc.v4.create_release.make_var_annot_hists) log_field_validation_results() (in module gnomad_qc.v5.data_ingestion.federated_validity_checks) low_quality_samples (in module gnomad_qc.v5.resources.meta)

M

main() (in module gnomad_qc.analyses.compute_pext) (in module gnomad_qc.v4.annotations.compute_coverage) (in module gnomad_qc.v4.annotations.fix_freq_an) (in module gnomad_qc.v4.annotations.generate_freq) (in module gnomad_qc.v4.annotations.generate_freq_genomes) (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations) (in module gnomad_qc.v4.annotations.insilico_predictors) (in module gnomad_qc.v4.annotations.vep_context_ht) (in module gnomad_qc.v4.annotations.vrs_annotation_batch) (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) (in module gnomad_qc.v4.assessment.summary_stats) (in module gnomad_qc.v4.create_release.create_combined_faf_release_ht) (in module gnomad_qc.v4.create_release.create_de_novo_release) (in module gnomad_qc.v4.create_release.create_false_dup_liftover) (in module gnomad_qc.v4.create_release.create_release_sites_ht) (in module gnomad_qc.v4.create_release.make_var_annot_hists) (in module gnomad_qc.v4.create_release.validate_and_export_vcf) (in module gnomad_qc.v4.sample_qc.assign_ancestry) (in module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht) (in module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht_genomes) (in module gnomad_qc.v4.sample_qc.generate_qc_mt) (in module gnomad_qc.v4.sample_qc.hard_filters) (in module gnomad_qc.v4.sample_qc.identify_trios) (in module gnomad_qc.v4.sample_qc.interval_qc) (in module gnomad_qc.v4.sample_qc.outlier_filtering) (in module gnomad_qc.v4.sample_qc.platform_inference) (in module gnomad_qc.v4.sample_qc.relatedness) (in module gnomad_qc.v4.sample_qc.sex_inference) (in module gnomad_qc.v4.subset) (in module gnomad_qc.v4.variant_qc.evaluation) (in module gnomad_qc.v4.variant_qc.final_filter) (in module gnomad_qc.v4.variant_qc.final_filter_genomes) (in module gnomad_qc.v4.variant_qc.import_variant_qc_vcf) (in module gnomad_qc.v4.variant_qc.random_forest) (in module gnomad_qc.v4.variant_qc.vqsr) (in module gnomad_qc.v5.data_ingestion.create_vds) (in module gnomad_qc.v5.data_ingestion.federated_validity_checks) make_info_expr() (in module gnomad_qc.v4.create_release.validate_and_export_vcf) make_vqsr_jobs() (in module gnomad_qc.v4.variant_qc.vqsr) MAP_FILTER_FIELD_TO_META (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) meta() (in module gnomad_qc.v4.resources.meta) meta_tsv_path() (in module gnomad_qc.v4.resources.meta) module gnomad_qc.analyses.compute_pext gnomad_qc.analyses.resources gnomad_qc.v4.annotations.compute_coverage gnomad_qc.v4.annotations.fix_freq_an gnomad_qc.v4.annotations.generate_freq gnomad_qc.v4.annotations.generate_freq_genomes gnomad_qc.v4.annotations.generate_variant_qc_annotations gnomad_qc.v4.annotations.insilico_predictors gnomad_qc.v4.annotations.vep_context_ht gnomad_qc.v4.annotations.vrs_annotation_batch gnomad_qc.v4.assessment.calculate_per_sample_stats gnomad_qc.v4.assessment.summary_stats gnomad_qc.v4.create_release.create_combined_faf_release_ht gnomad_qc.v4.create_release.create_de_novo_release gnomad_qc.v4.create_release.create_false_dup_liftover gnomad_qc.v4.create_release.create_release_sites_ht gnomad_qc.v4.create_release.create_release_utils gnomad_qc.v4.create_release.make_var_annot_hists gnomad_qc.v4.create_release.validate_and_export_vcf gnomad_qc.v4.resources.annotations gnomad_qc.v4.resources.assessment gnomad_qc.v4.resources.basics gnomad_qc.v4.resources.constants gnomad_qc.v4.resources.meta gnomad_qc.v4.resources.release gnomad_qc.v4.resources.sample_qc gnomad_qc.v4.resources.variant_qc gnomad_qc.v4.sample_qc.assign_ancestry gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht_genomes gnomad_qc.v4.sample_qc.generate_qc_mt gnomad_qc.v4.sample_qc.hard_filters gnomad_qc.v4.sample_qc.identify_trios gnomad_qc.v4.sample_qc.interval_qc gnomad_qc.v4.sample_qc.outlier_filtering gnomad_qc.v4.sample_qc.platform_inference gnomad_qc.v4.sample_qc.relatedness gnomad_qc.v4.sample_qc.sex_inference gnomad_qc.v4.subset gnomad_qc.v4.variant_qc.evaluation gnomad_qc.v4.variant_qc.final_filter gnomad_qc.v4.variant_qc.final_filter_genomes gnomad_qc.v4.variant_qc.import_variant_qc_vcf gnomad_qc.v4.variant_qc.random_forest gnomad_qc.v4.variant_qc.vqsr gnomad_qc.v5.configs.validity_inputs_schema gnomad_qc.v5.data_ingestion.create_vds gnomad_qc.v5.data_ingestion.federated_validity_checks gnomad_qc.v5.data_ingestion.field_md_to_html gnomad_qc.v5.resources.basics gnomad_qc.v5.resources.constants gnomad_qc.v5.resources.meta gnomad_qc.v5.resources.rwb_utils gnomad_qc.v5.resources.sample_qc

mt_hists_fields() (in module gnomad_qc.v4.annotations.generate_freq)

N

N_DIFF_SAMPLES (in module gnomad_qc.v4.sample_qc.create_sample_qc_metadata_ht_genomes) NA12878 (in module gnomad_qc.v4.resources.variant_qc) nearest_neighbors() (in module gnomad_qc.v4.resources.sample_qc) (in module gnomad_qc.v5.resources.sample_qc)

nearest_neighbors_filtering() (in module gnomad_qc.v4.resources.sample_qc) (in module gnomad_qc.v5.resources.sample_qc) NON_INFO_FEATURES (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations)

O

output_filename (gnomad_qc.v4.subset.ProcessingConfig attribute) output_partitions (gnomad_qc.v4.subset.ProcessingConfig attribute) output_path (gnomad_qc.v4.subset.ProcessingConfig attribute)

output_vcf (gnomad_qc.v4.subset.ProcessingConfig attribute) output_vds (gnomad_qc.v4.subset.ProcessingConfig attribute) overwrite (gnomad_qc.v4.subset.ProcessingConfig attribute)

P

parse_field_necessity_from_md() (in module gnomad_qc.v5.data_ingestion.federated_validity_checks) pass_only (gnomad_qc.v4.subset.ProcessingConfig attribute) patch_v4_genomes_callstats() (in module gnomad_qc.v4.annotations.generate_freq_genomes) pc_relate_pca_scores() (in module gnomad_qc.v4.resources.sample_qc) ped_filter_param_json_path() (in module gnomad_qc.v4.resources.sample_qc) ped_mendel_errors() (in module gnomad_qc.v4.resources.sample_qc) pedigree() (in module gnomad_qc.v4.resources.sample_qc) per_grp_min_rf_probs_json_path() (in module gnomad_qc.v5.resources.sample_qc) per_pop_min_rf_probs_json_path() (in module gnomad_qc.v4.resources.sample_qc) perform_cmh_test() (in module gnomad_qc.v4.create_release.create_combined_faf_release_ht) perform_contingency_table_test() (in module gnomad_qc.v4.create_release.create_combined_faf_release_ht) platform_table_to_dict() (in module gnomad_qc.v4.sample_qc.identify_trios) POP_MAP (in module gnomad_qc.v4.annotations.generate_freq_genomes)

pop_rf_path() (in module gnomad_qc.v4.resources.sample_qc) populate_info_dict() (in module gnomad_qc.v4.create_release.validate_and_export_vcf) populate_subset_info_dict() (in module gnomad_qc.v4.create_release.validate_and_export_vcf) prep_ht_for_rf() (in module gnomad_qc.v4.sample_qc.assign_ancestry) prep_vds_for_all_sites_stats() (in module gnomad_qc.v4.annotations.fix_freq_an) prepare_ht_for_validation() (in module gnomad_qc.v4.create_release.validate_and_export_vcf) prepare_sex_imputation_coverage_mt() (in module gnomad_qc.v4.sample_qc.sex_inference) prepare_vcf_header_dict() (in module gnomad_qc.v4.create_release.validate_and_export_vcf) print_cuking_command() (in module gnomad_qc.v4.sample_qc.relatedness) process_metadata_export() (in module gnomad_qc.v4.subset) process_score_cutoffs() (in module gnomad_qc.v4.variant_qc.final_filter) process_test_args() (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) process_vep_csq_header() (in module gnomad_qc.v4.create_release.validate_and_export_vcf) ProcessingConfig (class in gnomad_qc.v4.subset)

Q

qc_temp_prefix() (in module gnomad_qc.v4.resources.basics) (in module gnomad_qc.v5.resources.basics)

QUAL_HISTS (in module gnomad_qc.v4.annotations.generate_freq) qual_hists_json_path() (in module gnomad_qc.v4.resources.release)

R

recompute_as_qualapprox_from_lpl() (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations) reformat_ploidy_cutoffs_for_json() (in module gnomad_qc.v4.sample_qc.sex_inference) REGION_INFO_FIELDS (in module gnomad_qc.v4.variant_qc.final_filter) (in module gnomad_qc.v4.variant_qc.final_filter_genomes) regressed_filtering() (in module gnomad_qc.v4.resources.sample_qc) (in module gnomad_qc.v5.resources.sample_qc) related_samples_to_drop() (in module gnomad_qc.v4.resources.sample_qc) (in module gnomad_qc.v5.resources.sample_qc) relatedness() (in module gnomad_qc.v4.resources.sample_qc) (in module gnomad_qc.v5.resources.sample_qc) release_all_sites_an() (in module gnomad_qc.v4.resources.release) release_all_sites_an_tsv_path() (in module gnomad_qc.v4.resources.release) release_coverage() (in module gnomad_qc.v4.resources.release) release_coverage_path() (in module gnomad_qc.v4.resources.release) release_coverage_tsv_path() (in module gnomad_qc.v4.resources.release) release_de_novo() (in module gnomad_qc.v4.resources.release)

release_header_path() (in module gnomad_qc.v4.resources.release) release_ht_path() (in module gnomad_qc.v4.resources.release) release_lof() (in module gnomad_qc.v4.resources.assessment) release_sites() (in module gnomad_qc.v4.resources.release) release_summary_stats() (in module gnomad_qc.v4.resources.assessment) release_vcf_path() (in module gnomad_qc.v4.resources.release) remove_missing_vep_fields() (in module gnomad_qc.v4.create_release.create_release_utils) rep_on_read_partitions (gnomad_qc.v4.subset.ProcessingConfig attribute) restart_kernel_with_gnomad_packages() (in module gnomad_qc.v5.resources.rwb_utils) restructure_for_tsv() (in module gnomad_qc.v4.create_release.create_de_novo_release) run_compute_info() (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations) run_compute_related_samples_to_drop() (in module gnomad_qc.v4.sample_qc.relatedness) run_create_fake_pedigree() (in module gnomad_qc.v4.sample_qc.identify_trios) run_generate_sib_stats() (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations) run_generate_trio_stats() (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations) run_mendel_errors() (in module gnomad_qc.v4.sample_qc.identify_trios) run_pca() (in module gnomad_qc.v4.sample_qc.assign_ancestry)

S

sample_rankings() (in module gnomad_qc.v4.resources.sample_qc) (in module gnomad_qc.v5.resources.sample_qc) samples_to_exclude (in module gnomad_qc.v5.resources.meta) score_bin_validity_check() (in module gnomad_qc.v4.variant_qc.evaluation) select_type_from_joint_ht() (in module gnomad_qc.v4.create_release.validate_and_export_vcf) set_downsampling_freq_missing() (in module gnomad_qc.v4.annotations.generate_freq_genomes) snps_variant_recalibrator() (in module gnomad_qc.v4.variant_qc.vqsr) snps_variant_recalibrator_create_model() (in module gnomad_qc.v4.variant_qc.vqsr) split_info() (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations) split_intervals() (in module gnomad_qc.v4.variant_qc.vqsr)

split_multi (gnomad_qc.v4.subset.ProcessingConfig attribute) split_vds() (in module gnomad_qc.v4.annotations.generate_freq) stratified_filtering() (in module gnomad_qc.v4.resources.sample_qc) (in module gnomad_qc.v5.resources.sample_qc) SUBSET_DICT (in module gnomad_qc.v4.annotations.generate_freq) subset_samples (gnomad_qc.v4.subset.ProcessingConfig attribute) subset_workspaces (gnomad_qc.v4.subset.ProcessingConfig attribute) SUBSETS (in module gnomad_qc.v4.annotations.generate_freq_genomes) SUM_STAT_FILTERS (in module gnomad_qc.v4.assessment.calculate_per_sample_stats) SYNDIP (in module gnomad_qc.v4.resources.variant_qc)

T

test (gnomad_qc.v4.subset.ProcessingConfig attribute) tmp_dir (gnomad_qc.v4.subset.ProcessingConfig attribute) train_rf() (in module gnomad_qc.v4.variant_qc.random_forest) TRAINING_INFO_FIELDS (in module gnomad_qc.v4.variant_qc.final_filter) trio_denovo_ht() (in module gnomad_qc.v4.resources.sample_qc)

trios() (in module gnomad_qc.v4.resources.sample_qc) TRUTH_DATA (in module gnomad_qc.v4.annotations.generate_variant_qc_annotations) TRUTH_SAMPLES (in module gnomad_qc.v4.resources.variant_qc) TRUTH_SET_FIELDS (in module gnomad_qc.v4.variant_qc.final_filter) (in module gnomad_qc.v4.variant_qc.final_filter_genomes)

U

UKB_NA12878 (in module gnomad_qc.v4.resources.variant_qc) unfurl_nested_annotations() (in module gnomad_qc.v4.create_release.validate_and_export_vcf)

update_freq_an_and_hists() (in module gnomad_qc.v4.annotations.fix_freq_an) update_non_ukb_freq_ht() (in module gnomad_qc.v4.annotations.generate_freq) update_pop_labels() (in module gnomad_qc.v4.annotations.generate_freq_genomes)

V

V3_SPIKE_PROJECTS (in module gnomad_qc.v4.sample_qc.assign_ancestry) V4_POP_SPIKE_DICT (in module gnomad_qc.v4.sample_qc.assign_ancestry) validate_config() (in module gnomad_qc.v5.data_ingestion.federated_validity_checks) validate_config_fields_in_ht() (in module gnomad_qc.v5.data_ingestion.federated_validity_checks) validate_federated_data() (in module gnomad_qc.v5.data_ingestion.federated_validity_checks) validate_required_fields() (in module gnomad_qc.v5.data_ingestion.federated_validity_checks)

validate_vep_path() (in module gnomad_qc.v4.resources.annotations) validated_release_ht() (in module gnomad_qc.v4.resources.release) variant_qc_annotations (gnomad_qc.v4.subset.ProcessingConfig attribute) VARIANT_QC_GLOBAL_FIELDS (in module gnomad_qc.v4.variant_qc.final_filter) (in module gnomad_qc.v4.variant_qc.final_filter_genomes) VARIANT_QC_RESULT_FIELDS (in module gnomad_qc.v4.variant_qc.final_filter) VQSR_FEATURES (in module gnomad_qc.v4.resources.variant_qc)

W

write_pca_results() (in module gnomad_qc.v4.sample_qc.assign_ancestry)