gnomad_annotation_pext

  • Versions: 2.1.1

  • Reference genome builds: GRCh37

  • Type: hail.Table

Schema (2.1.1, GRCh37)

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Global fields:
    None
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Row fields:
    'context': 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
    }
    'locus': locus<GRCh37>
    'alleles': array<str>
    'a_index': int32
    'was_split': bool
    'methylation': struct {
        NUM: int32,
        MEAN: float64,
        GTE50: int32,
        GTE60: int32,
        GTE70: int32,
        GTE80: int32,
        GTE90: int32,
        GTE100: int32
    }
    'coverage': struct {
        exomes: struct {
            row_id: int64,
            mean: float64,
            median: int32,
            over_1: float64,
            over_5: float64,
            over_10: float64,
            over_15: float64,
            over_20: float64,
            over_25: float64,
            over_30: float64,
            over_50: float64,
            over_100: float64
        },
        genomes: struct {
            row_id: int64,
            mean: float64,
            median: int32,
            over_1: float64,
            over_5: float64,
            over_10: float64,
            over_15: float64,
            over_20: float64,
            over_25: float64,
            over_30: float64,
            over_50: float64,
            over_100: float64
        }
    }
    'gerp': float64
    'tx_annotation': array<struct {
        ensg: str,
        csq: str,
        symbol: str,
        lof: str,
        lof_flag: str,
        Cells_Transformedfibroblasts: float64,
        Prostate: float64,
        Spleen: float64,
        Brain_FrontalCortex_BA9_: float64,
        SmallIntestine_TerminalIleum: float64,
        MinorSalivaryGland: float64,
        Artery_Coronary: float64,
        Skin_SunExposed_Lowerleg_: float64,
        Cells_EBV_transformedlymphocytes: float64,
        Brain_Hippocampus: float64,
        Esophagus_Muscularis: float64,
        Brain_Nucleusaccumbens_basalganglia_: float64,
        Artery_Tibial: float64,
        Brain_Hypothalamus: float64,
        Adipose_Visceral_Omentum_: float64,
        Cervix_Ectocervix: float64,
        Brain_Spinalcord_cervicalc_1_: float64,
        Brain_CerebellarHemisphere: float64,
        Nerve_Tibial: float64,
        Breast_MammaryTissue: float64,
        Liver: float64,
        Skin_NotSunExposed_Suprapubic_: float64,
        AdrenalGland: float64,
        Vagina: float64,
        Pancreas: float64,
        Lung: float64,
        FallopianTube: float64,
        Pituitary: float64,
        Muscle_Skeletal: float64,
        Colon_Transverse: float64,
        Artery_Aorta: float64,
        Heart_AtrialAppendage: float64,
        Adipose_Subcutaneous: float64,
        Esophagus_Mucosa: float64,
        Heart_LeftVentricle: float64,
        Brain_Cerebellum: float64,
        Brain_Cortex: float64,
        Thyroid: float64,
        Brain_Substantianigra: float64,
        Kidney_Cortex: float64,
        Uterus: float64,
        Stomach: float64,
        WholeBlood: float64,
        Bladder: float64,
        Brain_Anteriorcingulatecortex_BA24_: float64,
        Brain_Putamen_basalganglia_: float64,
        Brain_Caudate_basalganglia_: float64,
        Colon_Sigmoid: float64,
        Cervix_Endocervix: float64,
        Ovary: float64,
        Esophagus_GastroesophagealJunction: float64,
        Testis: float64,
        Brain_Amygdala: float64,
        mean_proportion: float64
    }>
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Key: ['locus', 'alleles']
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