panukb_meta_analysis_high_quality
Versions: 0.3
Reference genome builds: GRCh37
Type:
hail.MatrixTable
Schema (0.3, GRCh37)
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Global fields:
None
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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>
}>
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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
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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
}>
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Column key: ['trait_type', 'phenocode', 'pheno_sex', 'coding', 'modifier']
Row key: ['locus', 'alleles']
----------------------------------------