.. _panukb_meta_analysis_high_quality:

panukb_meta_analysis_high_quality
=================================

*  **Versions:** 0.3
*  **Reference genome builds:** GRCh37
*  **Type:** :class:`hail.MatrixTable`

Schema (0.3, GRCh37)
~~~~~~~~~~~~~~~~~~~~

.. code-block:: text

    ----------------------------------------
    Global fields:
        None
    ----------------------------------------
    Column fields:
        'trait_type': str
        'phenocode': str
        'pheno_sex': str
        'coding': str
        'modifier': str
        'pheno_data': array<struct {
            n_cases: int32, 
            n_controls: int32, 
            heritability: struct {
                estimates: struct {
                    ldsc: struct {
                        h2_liability: float64, 
                        h2_liability_se: float64, 
                        h2_z: float64, 
                        h2_observed: float64, 
                        h2_observed_se: float64, 
                        intercept: float64, 
                        intercept_se: float64, 
                        ratio: float64, 
                        ratio_se: float64
                    }, 
                    sldsc_25bin: struct {
                        h2_liability: float64, 
                        h2_liability_se: float64, 
                        h2_z: float64, 
                        h2_observed: float64, 
                        h2_observed_se: float64, 
                        intercept: float64, 
                        intercept_se: float64, 
                        ratio: float64, 
                        ratio_se: float64
                    }, 
                    rhemc_25bin: struct {
                        h2_liability: float64, 
                        h2_liability_se: float64, 
                        h2_z: float64, 
                        h2_observed: float64, 
                        h2_observed_se: float64
                    }, 
                    rhemc_8bin: struct {
                        h2_liability: float64, 
                        h2_liability_se: float64, 
                        h2_observed: float64, 
                        h2_observed_se: float64, 
                        h2_z: float64
                    }, 
                    rhemc_25bin_50rv: struct {
                        h2_observed: float64, 
                        h2_observed_se: float64, 
                        h2_liability: float64, 
                        h2_liability_se: float64, 
                        h2_z: float64
                    }, 
                    final: struct {
                        h2_observed: float64, 
                        h2_observed_se: float64, 
                        h2_liability: float64, 
                        h2_liability_se: float64, 
                        h2_z: float64
                    }
                }, 
                qcflags: struct {
                    GWAS_run: bool, 
                    ancestry_reasonable_n: bool, 
                    defined_h2: bool, 
                    significant_z: bool, 
                    in_bounds_h2: bool, 
                    normal_lambda: bool, 
                    normal_ratio: bool, 
                    EUR_plus_1: bool, 
                    pass_all: bool
                }, 
                N_ancestry_QC_pass: int32
            }, 
            saige_version: str, 
            inv_normalized: bool, 
            pop: str, 
            lambda_gc: float64, 
            n_variants: int64, 
            n_sig_variants: int64, 
            saige_heritability: float64
        }>
        'description': str
        'description_more': str
        'coding_description': str
        'category': str
        'n_cases_full_cohort_both_sexes': int64
        'n_cases_full_cohort_females': int64
        'n_cases_full_cohort_males': int64
        'meta_analysis_data': array<struct {
            n_cases: int32, 
            n_controls: int32, 
            pop: array<str>
        }>
    ----------------------------------------
    Row fields:
        'locus': locus<GRCh37>
        'alleles': array<str>
        'rsid': str
        'varid': str
        'vep': struct {
            assembly_name: str, 
            allele_string: str, 
            ancestral: str, 
            colocated_variants: array<struct {
                aa_allele: str, 
                aa_maf: float64, 
                afr_allele: str, 
                afr_maf: float64, 
                allele_string: str, 
                amr_allele: str, 
                amr_maf: float64, 
                clin_sig: array<str>, 
                end: int32, 
                eas_allele: str, 
                eas_maf: float64, 
                ea_allele: str, 
                ea_maf: float64, 
                eur_allele: str, 
                eur_maf: float64, 
                exac_adj_allele: str, 
                exac_adj_maf: float64, 
                exac_allele: str, 
                exac_afr_allele: str, 
                exac_afr_maf: float64, 
                exac_amr_allele: str, 
                exac_amr_maf: float64, 
                exac_eas_allele: str, 
                exac_eas_maf: float64, 
                exac_fin_allele: str, 
                exac_fin_maf: float64, 
                exac_maf: float64, 
                exac_nfe_allele: str, 
                exac_nfe_maf: float64, 
                exac_oth_allele: str, 
                exac_oth_maf: float64, 
                exac_sas_allele: str, 
                exac_sas_maf: float64, 
                id: str, 
                minor_allele: str, 
                minor_allele_freq: float64, 
                phenotype_or_disease: int32, 
                pubmed: array<int32>, 
                sas_allele: str, 
                sas_maf: float64, 
                somatic: int32, 
                start: int32, 
                strand: int32
            }>, 
            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, 
                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, 
                uniparc: str, 
                variant_allele: str
            }>, 
            variant_class: str
        }
        'freq': array<struct {
            pop: str, 
            ac: float64, 
            af: float64, 
            an: int64, 
            gnomad_exomes_ac: int32, 
            gnomad_exomes_af: float64, 
            gnomad_exomes_an: int32, 
            gnomad_genomes_ac: int32, 
            gnomad_genomes_af: float64, 
            gnomad_genomes_an: int32
        }>
        'pass_gnomad_exomes': bool
        'pass_gnomad_genomes': bool
        'n_passing_populations': int32
        'high_quality': bool
        'nearest_genes': str
        'info': float64
    ----------------------------------------
    Entry fields:
        'meta_analysis': array<struct {
            BETA: float64, 
            SE: float64, 
            Pvalue: float64, 
            Q: float64, 
            Pvalue_het: float64, 
            N: int32, 
            N_pops: int32, 
            AF_Allele2: float64, 
            AF_Cases: float64, 
            AF_Controls: float64
        }>
    ----------------------------------------
    Column key: ['trait_type', 'phenocode', 'pheno_sex', 'coding', 'modifier']
    Row key: ['locus', 'alleles']
    ----------------------------------------