gnomad_hgdp_1kg_callset

Schema (3.1, GRCh38)

----------------------------------------
Global fields:
    'global_annotation_descriptions': struct {
        sex_imputation_ploidy_cutoffs: struct {
            Description: str
        },
        population_inference_pca_metrics: struct {
            Description: str
        },
        hard_filter_cutoffs: struct {
            Description: str
        },
        cohort_freq_meta: struct {
            Description: str
        },
        gnomad_freq_meta: struct {
            Description: str
        },
        cohort_freq_index_dict: struct {
            Description: str
        },
        gnomad_freq_index_dict: struct {
            Description: str
        },
        gnomad_faf_index_dict: struct {
            Description: str
        },
        gnomad_faf_meta: struct {
            Description: str
        },
        vep_version: struct {
            Description: str
        },
        vep_csq_header: struct {
            Description: str
        },
        dbsnp_version: struct {
            Description: str
        },
        filtering_model: struct {
            Description: str,
            sub_globals: struct {
                model_name: struct {
                    Description: str
                },
                score_name: struct {
                    Description: str
                },
                snv_cutoff: struct {
                    Description: str,
                    sub_globals: struct {
                        bin: struct {
                            Description: str
                        },
                        min_score: struct {
                            Description: str
                        }
                    }
                },
                indel_cutoff: struct {
                    Description: str,
                    sub_globals: struct {
                        bin: struct {
                            Description: str
                        },
                        min_score: struct {
                            Description: str
                        }
                    }
                },
                snv_training_variables: struct {
                    Description: str
                },
                indel_training_variables: struct {
                    Description: str
                }
            }
        },
        inbreeding_coeff_cutoff: 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
                }
            }
        },
        subsets: struct {
            Description: str,
            sub_annotations: struct {
                tgp: struct {
                    Description: str
                },
                hgdp: struct {
                    Description: str
                }
            }
        },
        sex_imputation: struct {
            Description: str,
            sub_annotations: struct {
                f_stat: struct {
                    Description: str
                },
                n_called: struct {
                    Description: str
                },
                expected_homs: struct {
                    Description: str
                },
                observed_homs: struct {
                    Description: str
                },
                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
                }
            }
        },
        sample_qc: struct {
            Description: str,
            sub_annotations: struct {
                n_hom_ref: struct {
                    Description: str
                },
                n_het: struct {
                    Description: str
                },
                n_hom_var: struct {
                    Description: str
                },
                n_non_ref: struct {
                    Description: str
                },
                n_snp: struct {
                    Description: str
                },
                n_insertion: struct {
                    Description: str
                },
                n_deletion: struct {
                    Description: str
                },
                n_transition: struct {
                    Description: str
                },
                n_transversion: struct {
                    Description: str
                },
                r_ti_tv: struct {
                    Description: str
                },
                r_het_hom_var: struct {
                    Description: str
                },
                r_insertion_deletion: struct {
                    Description: str
                }
            }
        },
        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
                }
            }
        },
        labeled_subpop: struct {
            Description: str
        },
        gnomad_release: struct {
            Description: str
        }
    }
    '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
    }
    'population_inference_pca_metrics': struct {
        n_pcs: int32,
        min_prob: float64
    }
    '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
    }
    'cohort_freq_meta': array<dict<str, str>>
    'cohort_freq_index_dict': dict<str, int32>
    'gnomad_freq_meta': array<dict<str, str>>
    'gnomad_freq_index_dict': dict<str, int32>
    'gnomad_faf_index_dict': dict<str, int32>
    'gnomad_faf_meta': array<dict<str, str>>
    'vep_version': str
    'vep_csq_header': str
    'dbsnp_version': str
    'filtering_model': struct {
        model_name: str,
        score_name: str,
        snv_cutoff: struct {
            bin: float64,
            min_score: float64
        },
        indel_cutoff: struct {
            bin: float64,
            min_score: float64
        },
        snv_training_variables: array<str>,
        indel_training_variables: array<str>
    }
    'inbreeding_coeff_cutoff': float64
----------------------------------------
Column 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
    }
    'subsets': struct {
        tgp: bool,
        hgdp: bool
    }
    '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,
        impute_sex_stats: struct {
            f_stat: float64,
            n_called: int64,
            expected_homs: float64,
            observed_homs: int64
        }
    }
    'sample_qc': struct {
        n_hom_ref: int64,
        n_het: int64,
        n_hom_var: int64,
        n_non_ref: int64,
        n_snp: int64,
        n_insertion: int64,
        n_deletion: int64,
        n_transition: int64,
        n_transversion: int64,
        r_ti_tv: float64,
        r_het_hom_var: float64,
        r_insertion_deletion: float64
    }
    '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
    }
    'labeled_subpop': str
    'gnomad_release': bool
----------------------------------------
Row fields:
    'locus': locus<GRCh38>
    'alleles': array<str>
    'rsid': str
    'AS_lowqual': bool
    'telomere_or_centromere': bool
    'cohort_freq': array<struct {
        AC: int32,
        AF: float64,
        AN: int32,
        homozygote_count: int32
    }>
    'gnomad_freq': array<struct {
        AC: int32,
        AF: float64,
        AN: int32,
        homozygote_count: int32
    }>
    'gnomad_raw_qual_hists': struct {
        gq_hist_all: struct {
            bin_edges: array<float64>,
            bin_freq: array<int64>,
            n_smaller: int64,
            n_larger: int64
        },
        dp_hist_all: struct {
            bin_edges: array<float64>,
            bin_freq: array<int64>,
            n_smaller: int64,
            n_larger: int64
        },
        gq_hist_alt: struct {
            bin_edges: array<float64>,
            bin_freq: array<int64>,
            n_smaller: int64,
            n_larger: int64
        },
        dp_hist_alt: struct {
            bin_edges: array<float64>,
            bin_freq: array<int64>,
            n_smaller: int64,
            n_larger: int64
        },
        ab_hist_alt: struct {
            bin_edges: array<float64>,
            bin_freq: array<int64>,
            n_smaller: int64,
            n_larger: int64
        }
    }
    'gnomad_popmax': struct {
        AC: int32,
        AF: float64,
        AN: int32,
        homozygote_count: int32,
        pop: str,
        faf95: float64
    }
    'gnomad_qual_hists': struct {
        gq_hist_all: struct {
            bin_edges: array<float64>,
            bin_freq: array<int64>,
            n_smaller: int64,
            n_larger: int64
        },
        dp_hist_all: struct {
            bin_edges: array<float64>,
            bin_freq: array<int64>,
            n_smaller: int64,
            n_larger: int64
        },
        gq_hist_alt: struct {
            bin_edges: array<float64>,
            bin_freq: array<int64>,
            n_smaller: int64,
            n_larger: int64
        },
        dp_hist_alt: struct {
            bin_edges: array<float64>,
            bin_freq: array<int64>,
            n_smaller: int64,
            n_larger: int64
        },
        ab_hist_alt: struct {
            bin_edges: array<float64>,
            bin_freq: array<int64>,
            n_smaller: int64,
            n_larger: int64
        }
    }
    'gnomad_faf': array<struct {
        faf95: float64,
        faf99: float64
    }>
    'filters': set<str>
    'info': struct {
        QUALapprox: int64,
        SB: array<int32>,
        MQ: float64,
        MQRankSum: float64,
        VarDP: int32,
        AS_ReadPosRankSum: float64,
        AS_pab_max: float64,
        AS_QD: float32,
        AS_MQ: float64,
        QD: float32,
        AS_MQRankSum: float64,
        FS: float64,
        AS_FS: float64,
        ReadPosRankSum: float64,
        AS_QUALapprox: int64,
        AS_SB_TABLE: array<int32>,
        AS_VarDP: int32,
        AS_SOR: float64,
        SOR: float64,
        transmitted_singleton: bool,
        omni: bool,
        mills: bool,
        monoallelic: bool,
        AS_VQSLOD: float64,
        InbreedingCoeff: float32
    }
    'vep': struct {
        assembly_name: str,
        allele_string: str,
        ancestral: str,
        context: str,
        end: int32,
        id: str,
        input: str,
        intergenic_consequences: array<struct {
            allele_num: int32,
            consequence_terms: array<str>,
            impact: str,
            minimised: int32,
            variant_allele: str
        }>,
        most_severe_consequence: str,
        motif_feature_consequences: array<struct {
            allele_num: int32,
            consequence_terms: array<str>,
            high_inf_pos: str,
            impact: str,
            minimised: int32,
            motif_feature_id: str,
            motif_name: str,
            motif_pos: int32,
            motif_score_change: float64,
            strand: int32,
            variant_allele: str
        }>,
        regulatory_feature_consequences: array<struct {
            allele_num: int32,
            biotype: str,
            consequence_terms: array<str>,
            impact: str,
            minimised: int32,
            regulatory_feature_id: str,
            variant_allele: str
        }>,
        seq_region_name: str,
        start: int32,
        strand: int32,
        transcript_consequences: array<struct {
            allele_num: int32,
            amino_acids: str,
            appris: str,
            biotype: str,
            canonical: int32,
            ccds: str,
            cdna_start: int32,
            cdna_end: int32,
            cds_end: int32,
            cds_start: int32,
            codons: str,
            consequence_terms: array<str>,
            distance: int32,
            domains: array<struct {
                db: str,
                name: str
            }>,
            exon: str,
            gene_id: str,
            gene_pheno: int32,
            gene_symbol: str,
            gene_symbol_source: str,
            hgnc_id: str,
            hgvsc: str,
            hgvsp: str,
            hgvs_offset: int32,
            impact: str,
            intron: str,
            lof: str,
            lof_flags: str,
            lof_filter: str,
            lof_info: str,
            minimised: int32,
            polyphen_prediction: str,
            polyphen_score: float64,
            protein_end: int32,
            protein_start: int32,
            protein_id: str,
            sift_prediction: str,
            sift_score: float64,
            strand: int32,
            swissprot: str,
            transcript_id: str,
            trembl: str,
            tsl: int32,
            uniparc: str,
            variant_allele: str
        }>,
        variant_class: str
    }
    'vqsr': struct {
        AS_VQSLOD: float64,
        AS_culprit: str,
        NEGATIVE_TRAIN_SITE: bool,
        POSITIVE_TRAIN_SITE: bool
    }
    'region_flag': struct {
        lcr: bool,
        segdup: bool
    }
    'allele_info': struct {
        variant_type: str,
        allele_type: str,
        n_alt_alleles: int32,
        was_mixed: bool
    }
    'cadd': struct {
        raw_score: float32,
        phred: float32
    }
    'revel': struct {
        revel_score: float64,
        ref_aa: str,
        alt_aa: str
    }
    'splice_ai': struct {
        splice_ai: array<float32>,
        max_ds: float32,
        splice_consequence: str
    }
    'primate_ai': struct {
        primate_ai_score: float32
    }
----------------------------------------
Entry fields:
    'END': int32
    'DP': int32
    'GQ': int32
    'MIN_DP': int32
    'PID': str
    'RGQ': int32
    'SB': array<int32>
    'GT': call
    'PGT': call
    'AD': array<int32>
    'PL': array<int32>
----------------------------------------
Column key: ['s']
Row key: ['locus', 'alleles']
----------------------------------------