gnomad_exome_sites
Versions: 2.1.1
Reference genome builds: GRCh37, GRCh38
Type:
hail.Table
Schema (2.1.1, GRCh37)
----------------------------------------
Global fields:
'rf': struct {
variants_by_type: dict<str, int32>,
feature_medians: dict<str, struct {
variant_type: str,
n_alt_alleles: int32,
qd: float64,
pab_max: float64,
info_MQRankSum: float64,
info_SOR: float64,
info_InbreedingCoeff: float64,
info_ReadPosRankSum: float64,
info_FS: float64,
info_QD: float64,
info_MQ: float64,
info_DP: int32
}>,
test_intervals: array<interval<locus<GRCh37>>>,
test_results: array<struct {
rf_prediction: str,
rf_label: str,
n: int32
}>,
features_importance: dict<str, float64>,
features: array<str>,
vqsr_training: bool,
no_transmitted_singletons: bool,
adj: bool,
rf_hash: str,
rf_snv_cutoff: struct {
bin: int32,
min_score: float64
},
rf_indel_cutoff: struct {
bin: int32,
min_score: float64
}
}
'freq_meta': array<dict<str, str>>
'freq_index_dict': dict<str, int32>
'popmax_index_dict': dict<str, int32>
'age_index_dict': dict<str, int32>
'faf_index_dict': dict<str, int32>
'age_distribution': array<int32>
----------------------------------------
Row fields:
'locus': locus<GRCh37>
'alleles': array<str>
'freq': array<struct {
AC: int32,
AF: float64,
AN: int32,
homozygote_count: int32
}>
'age_hist_het': array<struct {
bin_edges: array<float64>,
bin_freq: array<int64>,
n_smaller: int64,
n_larger: int64
}>
'age_hist_hom': array<struct {
bin_edges: array<float64>,
bin_freq: array<int64>,
n_smaller: int64,
n_larger: int64
}>
'popmax': array<struct {
AC: int32,
AF: float64,
AN: int32,
homozygote_count: int32,
pop: str
}>
'faf': array<struct {
meta: dict<str, str>,
faf95: float64,
faf99: float64
}>
'lcr': bool
'decoy': bool
'segdup': bool
'nonpar': bool
'variant_type': str
'allele_type': str
'n_alt_alleles': int32
'was_mixed': bool
'has_star': bool
'qd': float64
'pab_max': float64
'info_MQRankSum': float64
'info_SOR': float64
'info_InbreedingCoeff': float64
'info_ReadPosRankSum': float64
'info_FS': float64
'info_QD': float64
'info_MQ': float64
'info_DP': int32
'transmitted_singleton': bool
'fail_hard_filters': bool
'info_POSITIVE_TRAIN_SITE': bool
'info_NEGATIVE_TRAIN_SITE': bool
'omni': bool
'mills': bool
'n_nonref': int32
'tp': bool
'rf_train': bool
'rf_label': str
'rf_probability': float64
'singleton': bool
'was_split': bool
'score': float64
'rank': int64
'singleton_rank': int64
'biallelic_rank': int64
'adj_biallelic_singleton_rank': int64
'adj_rank': int64
'adj_biallelic_rank': int64
'adj_singleton_rank': int64
'biallelic_singleton_rank': int64
'filters': set<str>
'gq_hist_alt': struct {
bin_edges: array<float64>,
bin_freq: array<int64>,
n_smaller: int64,
n_larger: int64
}
'gq_hist_all': 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
}
'dp_hist_all': 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
}
'qual': float64
'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
}
'allele_info': struct {
BaseQRankSum: float64,
ClippingRankSum: float64,
DB: bool,
DP: int32,
DS: bool,
END: int32,
FS: float64,
HaplotypeScore: float64,
InbreedingCoeff: float64,
MQ: float64,
MQRankSum: float64,
NEGATIVE_TRAIN_SITE: bool,
POSITIVE_TRAIN_SITE: bool,
QD: float64,
ReadPosRankSum: float64,
SOR: float64,
VQSLOD: float64,
culprit: str
}
'rsid': str
----------------------------------------
Key: ['locus', 'alleles']
----------------------------------------