gnomad.sample_qc

• ancestry
  • pc_project()
  • apply_onnx_classification_model()
  • apply_sklearn_classification_model()
  • convert_sklearn_rf_to_onnx()
  • assign_population_pcs()
  • run_pca_with_relateds()
• filtering
  • compute_qc_metrics_residuals()
  • compute_stratified_metrics_filter()
  • compute_stratified_sample_qc()
  • merge_sample_qc_expr()
  • determine_nearest_neighbors()
• pipeline
  • filter_rows_for_qc()
  • get_qc_mt()
  • infer_sex_karyotype()
  • annotate_sex()
• platform
  • compute_callrate_mt()
  • run_platform_pca()
  • assign_platform_from_pcs()
• relatedness
  • UNRELATED
  • SECOND_DEGREE_RELATIVES
  • PARENT_CHILD
  • SIBLINGS
  • DUPLICATE_OR_TWINS
  • AMBIGUOUS_RELATIONSHIP
  • get_duplicated_samples()
  • get_duplicated_samples_ht()
  • explode_duplicate_samples_ht()
  • get_relationship_expr()
  • get_slope_int_relationship_expr()
  • infer_families()
  • create_fake_pedigree()
  • compute_related_samples_to_drop()
  • filter_to_trios()
  • generate_trio_stats_expr()
  • generate_sib_stats_expr()
• sex
  • adjusted_sex_ploidy_expr()
  • adjust_sex_ploidy()
  • gaussian_mixture_model_karyotype_assignment()
  • get_ploidy_cutoffs()
  • get_chr_x_hom_alt_cutoffs()
  • get_sex_expr()