gnomad_hgdp_1kg_subset_sample_metadata

  • Versions: 3.1.2

  • Reference genome builds: GRCh38

  • Type: hail.Table

Schema (3.1.2, GRCh38)

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Global fields:
    'global_annotation_descriptions': struct {
        gnomad_sex_imputation_ploidy_cutoffs: struct {
            Description: str
        },
        gnomad_population_inference_pca_metrics: struct {
            Description: str
        },
        sample_hard_filter_cutoffs: struct {
            Description: str
        },
        gnomad_sample_qc_metric_outlier_cutoffs: struct {
            Description: str
        },
        gnomad_age_distribution: struct {
            Description: str,
            sub_globals: struct {
                bin_edges: struct {
                    Description: str
                },
                bin_freq: struct {
                    Description: str
                },
                n_smaller: struct {
                    Description: str
                },
                n_larger: struct {
                    Description: str
                }
            }
        }
    }
    'sample_annotation_descriptions': struct {
        s: struct {
            Description: str
        },
        bam_metrics: struct {
            Description: str,
            sub_annotations: struct {
                pct_bases_20x: struct {
                    Description: str
                },
                pct_chimeras: struct {
                    Description: str
                },
                freemix: struct {
                    Description: str
                },
                mean_coverage: struct {
                    Description: str
                },
                median_coverage: struct {
                    Description: str
                },
                mean_insert_size: struct {
                    Description: str
                },
                median_insert_size: struct {
                    Description: str
                },
                pct_bases_10x: struct {
                    Description: str
                }
            }
        },
        sample_qc: struct {
            Description: str,
            sub_annotations: struct {
                n_deletion: struct {
                    Description: str
                },
                n_het: struct {
                    Description: str
                },
                n_hom_ref: struct {
                    Description: str
                },
                n_hom_var: struct {
                    Description: str
                },
                n_insertion: struct {
                    Description: str
                },
                n_non_ref: struct {
                    Description: str
                },
                n_snp: struct {
                    Description: str
                },
                n_transition: struct {
                    Description: str
                },
                n_transversion: struct {
                    Description: str
                },
                r_het_hom_var: struct {
                    Description: str
                },
                r_insertion_deletion: struct {
                    Description: str
                },
                r_ti_tv: struct {
                    Description: str
                }
            }
        },
        gnomad_sex_imputation: struct {
            Description: str,
            sub_annotations: struct {
                chr20_mean_dp: struct {
                    Description: str
                },
                chrX_mean_dp: struct {
                    Description: str
                },
                chrY_mean_dp: struct {
                    Description: str
                },
                chrX_ploidy: struct {
                    Description: str
                },
                chrY_ploidy: struct {
                    Description: str
                },
                X_karyotype: struct {
                    Description: str
                },
                Y_karyotype: struct {
                    Description: str
                },
                sex_karyotype: struct {
                    Description: str
                },
                f_stat: struct {
                    Description: str
                },
                n_called: struct {
                    Description: str
                },
                expected_homs: struct {
                    Description: str
                },
                observed_homs: struct {
                    Description: str
                }
            }
        },
        gnomad_population_inference: struct {
            Description: str,
            sub_annotations: struct {
                pca_scores: struct {
                    Description: str
                },
                pop: struct {
                    Description: str
                },
                prob_afr: struct {
                    Description: str
                },
                prob_ami: struct {
                    Description: str
                },
                prob_amr: struct {
                    Description: str
                },
                prob_asj: struct {
                    Description: str
                },
                prob_eas: struct {
                    Description: str
                },
                prob_fin: struct {
                    Description: str
                },
                prob_mid: struct {
                    Description: str
                },
                prob_nfe: struct {
                    Description: str
                },
                prob_oth: struct {
                    Description: str
                },
                prob_sas: struct {
                    Description: str
                }
            }
        },
        gnomad_sample_qc_residuals: struct {
            Description: tuple (
                str
            ),
            sub_annotations: struct {
                n_snp_residual: struct {
                    Description: str
                },
                r_ti_tv_residual: struct {
                    Description: str
                },
                r_insertion_deletion_residual: struct {
                    Description: str
                },
                n_insertion_residual: struct {
                    Description: str
                },
                n_deletion_residual: struct {
                    Description: str
                },
                r_het_hom_var_residual: struct {
                    Description: str
                },
                n_transition_residual: struct {
                    Description: str
                },
                n_transversion_residual: struct {
                    Description: str
                }
            }
        },
        gnomad_sample_filters: struct {
            Description: str,
            sub_annotations: struct {
                hard_filters: struct {
                    Description: str
                },
                hard_filtered: struct {
                    Description: str
                },
                release_related: struct {
                    Description: str
                },
                qc_metrics_filters: struct {
                    Description: str
                }
            }
        },
        gnomad_high_quality: struct {
            Description: str
        },
        gnomad_release: struct {
            Description: str
        },
        relatedness_inference: struct {
            Description: str,
            sub_annotations: struct {
                related_samples: struct {
                    Description: str,
                    sub_annotations: struct {
                        s: struct {
                            Description: str
                        },
                        kin: struct {
                            Description: str
                        },
                        ibd0: struct {
                            Description: str
                        },
                        ibd1: struct {
                            Description: str
                        },
                        ibd2: struct {
                            Description: str
                        }
                    }
                },
                related: struct {
                    Description: str
                }
            }
        },
        hgdp_tgp_meta: struct {
            Description: str,
            sub_annotations: struct {
                project: struct {
                    Description: str
                },
                study_region: struct {
                    Description: str
                },
                population: struct {
                    Description: str
                },
                genetic_region: struct {
                    Description: str
                },
                latitude: struct {
                    Description: str
                },
                longitude: struct {
                    Description: str
                },
                hgdp_technical_meta: struct {
                    Description: str,
                    sub_annotations: struct {
                        source: struct {
                            Description: str
                        },
                        library_type: struct {
                            Description: str
                        }
                    }
                },
                global_pca_scores: struct {
                    Description: str
                },
                subcontinental_pca: struct {
                    Description: str,
                    sub_annotations: struct {
                        pca_scores: struct {
                            Description: str
                        },
                        pca_scores_outliers_removed: struct {
                            Description: str
                        },
                        outlier: struct {
                            Description: str
                        }
                    }
                },
                gnomad_labeled_subpop: struct {
                    Description: str
                }
            }
        },
        high_quality: struct {
            Description: str
        }
    }
    'gnomad_sex_imputation_ploidy_cutoffs': struct {
        x_ploidy_cutoffs: struct {
            upper_cutoff_X: float64,
            lower_cutoff_XX: float64,
            upper_cutoff_XX: float64,
            lower_cutoff_XXX: float64
        },
        y_ploidy_cutoffs: struct {
            lower_cutoff_Y: float64,
            upper_cutoff_Y: float64,
            lower_cutoff_YY: float64
        },
        f_stat_cutoff: float64
    }
    'gnomad_population_inference_pca_metrics': struct {
        n_pcs: int32,
        min_prob: float64
    }
    'sample_hard_filter_cutoffs': struct {
        min_cov: int32,
        max_n_snp: float64,
        min_n_snp: float64,
        max_n_singleton: float64,
        max_r_het_hom_var: float64,
        max_pct_contamination: float64,
        max_pct_chimera: float64,
        min_median_insert_size: int32
    }
    'gnomad_sample_qc_metric_outlier_cutoffs': struct {
        lms: struct {
            n_snp: struct {
                beta: array<float64>,
                standard_error: array<float64>,
                t_stat: array<float64>,
                p_value: array<float64>,
                multiple_standard_error: float64,
                multiple_r_squared: float64,
                adjusted_r_squared: float64,
                f_stat: float64,
                multiple_p_value: float64,
                n: int32
            },
            n_singleton: struct {
                beta: array<float64>,
                standard_error: array<float64>,
                t_stat: array<float64>,
                p_value: array<float64>,
                multiple_standard_error: float64,
                multiple_r_squared: float64,
                adjusted_r_squared: float64,
                f_stat: float64,
                multiple_p_value: float64,
                n: int32
            },
            r_ti_tv: struct {
                beta: array<float64>,
                standard_error: array<float64>,
                t_stat: array<float64>,
                p_value: array<float64>,
                multiple_standard_error: float64,
                multiple_r_squared: float64,
                adjusted_r_squared: float64,
                f_stat: float64,
                multiple_p_value: float64,
                n: int32
            },
            r_insertion_deletion: struct {
                beta: array<float64>,
                standard_error: array<float64>,
                t_stat: array<float64>,
                p_value: array<float64>,
                multiple_standard_error: float64,
                multiple_r_squared: float64,
                adjusted_r_squared: float64,
                f_stat: float64,
                multiple_p_value: float64,
                n: int32
            },
            n_insertion: struct {
                beta: array<float64>,
                standard_error: array<float64>,
                t_stat: array<float64>,
                p_value: array<float64>,
                multiple_standard_error: float64,
                multiple_r_squared: float64,
                adjusted_r_squared: float64,
                f_stat: float64,
                multiple_p_value: float64,
                n: int32
            },
            n_deletion: struct {
                beta: array<float64>,
                standard_error: array<float64>,
                t_stat: array<float64>,
                p_value: array<float64>,
                multiple_standard_error: float64,
                multiple_r_squared: float64,
                adjusted_r_squared: float64,
                f_stat: float64,
                multiple_p_value: float64,
                n: int32
            },
            r_het_hom_var: struct {
                beta: array<float64>,
                standard_error: array<float64>,
                t_stat: array<float64>,
                p_value: array<float64>,
                multiple_standard_error: float64,
                multiple_r_squared: float64,
                adjusted_r_squared: float64,
                f_stat: float64,
                multiple_p_value: float64,
                n: int32
            },
            n_transition: struct {
                beta: array<float64>,
                standard_error: array<float64>,
                t_stat: array<float64>,
                p_value: array<float64>,
                multiple_standard_error: float64,
                multiple_r_squared: float64,
                adjusted_r_squared: float64,
                f_stat: float64,
                multiple_p_value: float64,
                n: int32
            },
            n_transversion: struct {
                beta: array<float64>,
                standard_error: array<float64>,
                t_stat: array<float64>,
                p_value: array<float64>,
                multiple_standard_error: float64,
                multiple_r_squared: float64,
                adjusted_r_squared: float64,
                f_stat: float64,
                multiple_p_value: float64,
                n: int32
            }
        },
        qc_metrics_stats: struct {
            n_snp_residual: struct {
                median: float64,
                mad: float64,
                lower: float64,
                upper: float64
            },
            n_singleton_residual: struct {
                median: float64,
                mad: float64,
                lower: float64,
                upper: float64
            },
            r_ti_tv_residual: struct {
                median: float64,
                mad: float64,
                lower: float64,
                upper: float64
            },
            r_insertion_deletion_residual: struct {
                median: float64,
                mad: float64,
                lower: float64,
                upper: float64
            },
            n_insertion_residual: struct {
                median: float64,
                mad: float64,
                lower: float64,
                upper: float64
            },
            n_deletion_residual: struct {
                median: float64,
                mad: float64,
                lower: float64,
                upper: float64
            },
            r_het_hom_var_residual: struct {
                median: float64,
                mad: float64,
                lower: float64,
                upper: float64
            },
            n_transition_residual: struct {
                median: float64,
                mad: float64,
                lower: float64,
                upper: float64
            },
            n_transversion_residual: struct {
                median: float64,
                mad: float64,
                lower: float64,
                upper: float64
            }
        },
        n_pcs: int32,
        used_regressed_metrics: bool
    }
    'gnomad_age_distribution': struct {
        bin_edges: array<float64>,
        bin_freq: array<int32>,
        n_smaller: int32,
        n_larger: int32
    }
----------------------------------------
Row fields:
    's': str
    'bam_metrics': struct {
        pct_bases_20x: float64,
        pct_chimeras: float64,
        freemix: float64,
        mean_coverage: float64,
        median_coverage: float64,
        mean_insert_size: float64,
        median_insert_size: float64,
        pct_bases_10x: float64
    }
    'sample_qc': struct {
        n_deletion: int64,
        n_het: int64,
        n_hom_ref: int64,
        n_hom_var: int64,
        n_insertion: int64,
        n_non_ref: int64,
        n_snp: int64,
        n_transition: int64,
        n_transversion: int64,
        r_het_hom_var: float64,
        r_insertion_deletion: float64,
        r_ti_tv: float64
    }
    'gnomad_sex_imputation': struct {
        chr20_mean_dp: float32,
        chrX_mean_dp: float32,
        chrY_mean_dp: float32,
        chrX_ploidy: float32,
        chrY_ploidy: float32,
        X_karyotype: str,
        Y_karyotype: str,
        sex_karyotype: str,
        f_stat: float64,
        n_called: int64,
        expected_homs: float64,
        observed_homs: int64
    }
    'gnomad_population_inference': struct {
        pca_scores: array<float64>,
        pop: str,
        prob_afr: float64,
        prob_ami: float64,
        prob_amr: float64,
        prob_asj: float64,
        prob_eas: float64,
        prob_fin: float64,
        prob_mid: float64,
        prob_nfe: float64,
        prob_oth: float64,
        prob_sas: float64
    }
    'gnomad_sample_qc_residuals': struct {
        n_snp_residual: float64,
        r_ti_tv_residual: float64,
        r_insertion_deletion_residual: float64,
        n_insertion_residual: float64,
        n_deletion_residual: float64,
        r_het_hom_var_residual: float64,
        n_transition_residual: float64,
        n_transversion_residual: float64
    }
    'gnomad_sample_filters': struct {
        hard_filters: set<str>,
        hard_filtered: bool,
        release_related: bool,
        qc_metrics_filters: set<str>
    }
    'gnomad_high_quality': bool
    'gnomad_release': bool
    'relatedness_inference': struct {
        related_samples: set<struct {
            s: str,
            kin: float64,
            ibd0: float64,
            ibd1: float64,
            ibd2: float64
        }>,
        related: bool
    }
    'hgdp_tgp_meta': struct {
        project: str,
        study_region: str,
        population: str,
        genetic_region: str,
        latitude: float64,
        longitude: float64,
        hgdp_technical_meta: struct {
            source: str,
            library_type: str
        },
        global_pca_scores: array<float64>,
        subcontinental_pca: struct {
            pca_scores: array<float64>,
            pca_scores_outliers_removed: array<float64>,
            outlier: bool
        },
        gnomad_labeled_subpop: str
    }
    'high_quality': bool
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Key: ['s']
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