gnomad_hgdp_1kg_subset_variant_annotations
Versions: 3.1.2
Reference genome builds: GRCh38
Type:
hail.Table
Schema (3.1.2, GRCh38)
----------------------------------------
Global fields:
'global_annotation_descriptions': struct {
hgdp_tgp_freq_meta: struct {
Description: str
},
gnomad_freq_meta: struct {
Description: str
},
hgdp_tgp_freq_index_dict: struct {
Description: str
},
gnomad_freq_index_dict: struct {
Description: str
},
gnomad_faf_meta: struct {
Description: str
},
gnomad_faf_index_dict: struct {
Description: str
},
variant_filtering_model: struct {
Description: set<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
}
}
},
variant_inbreeding_coeff_cutoff: struct {
Description: str
},
vep_version: struct {
Description: str
},
vep_csq_header: struct {
Description: str
},
dbsnp_version: struct {
Description: str
}
}
'variant_annotation_descriptions': struct {
locus: struct {
Description: str
},
alleles: struct {
Description: str
},
rsid: struct {
Description: str
},
a_index: struct {
Description: str
},
was_split: struct {
Description: str
},
hgdp_tgp_freq: struct {
Description: str,
sub_annotations: struct {
AC: struct {
Description: str
},
AF: struct {
Description: str
},
AN: struct {
Description: str
},
homozygote_count: struct {
Description: str
}
}
},
gnomad_freq: struct {
Description: str,
sub_annotations: struct {
AC: struct {
Description: str
},
AF: struct {
Description: str
},
AN: struct {
Description: str
},
homozygote_count: struct {
Description: str
}
}
},
gnomad_popmax: struct {
Description: str,
sub_annotations: struct {
AC: struct {
Description: str
},
AF: struct {
Description: str
},
AN: struct {
Description: str
},
homozygote_count: struct {
Description: str
},
pop: struct {
Description: str
},
faf95: struct {
Description: str
}
}
},
gnomad_faf: struct {
Description: str,
sub_annotations: struct {
faf95: struct {
Description: str
},
faf99: struct {
Description: str
}
}
},
gnomad_qual_hists: struct {
Description: str,
sub_annotations: struct {
gq_hist_all: struct {
Description: str,
sub_annotations: struct {
bin_edges: struct {
Description: str
},
bin_freq: struct {
Description: str
},
n_smaller: struct {
Description: str
},
n_larger: struct {
Description: str
}
}
},
dp_hist_all: struct {
Description: str,
sub_annotations: struct {
bin_edges: struct {
Description: str
},
bin_freq: struct {
Description: str
},
n_smaller: struct {
Description: str
},
n_larger: struct {
Description: str
}
}
},
gq_hist_alt: struct {
Description: str,
sub_annotations: struct {
bin_edges: struct {
Description: str
},
bin_freq: struct {
Description: str
},
n_smaller: struct {
Description: str
},
n_larger: struct {
Description: str
}
}
},
dp_hist_alt: struct {
Description: str,
sub_annotations: struct {
bin_edges: struct {
Description: str
},
bin_freq: struct {
Description: str
},
n_smaller: struct {
Description: str
},
n_larger: struct {
Description: str
}
}
},
ab_hist_alt: struct {
Description: str,
sub_annotations: struct {
bin_edges: struct {
Description: str
},
bin_freq: struct {
Description: str
},
n_smaller: struct {
Description: str
},
n_larger: struct {
Description: str
}
}
}
}
},
gnomad_raw_qual_hists: struct {
Description: str,
sub_annotations: struct {
gq_hist_all: struct {
Description: str,
sub_annotations: struct {
bin_edges: struct {
Description: str
},
bin_freq: struct {
Description: str
},
n_smaller: struct {
Description: str
},
n_larger: struct {
Description: str
}
}
},
dp_hist_all: struct {
Description: str,
sub_annotations: struct {
bin_edges: struct {
Description: str
},
bin_freq: struct {
Description: str
},
n_smaller: struct {
Description: str
},
n_larger: struct {
Description: str
}
}
},
gq_hist_alt: struct {
Description: str,
sub_annotations: struct {
bin_edges: struct {
Description: str
},
bin_freq: struct {
Description: str
},
n_smaller: struct {
Description: str
},
n_larger: struct {
Description: str
}
}
},
dp_hist_alt: struct {
Description: str,
sub_annotations: struct {
bin_edges: struct {
Description: str
},
bin_freq: struct {
Description: str
},
n_smaller: struct {
Description: str
},
n_larger: struct {
Description: str
}
}
},
ab_hist_alt: struct {
Description: str,
sub_annotations: struct {
bin_edges: struct {
Description: str
},
bin_freq: struct {
Description: str
},
n_smaller: struct {
Description: str
},
n_larger: struct {
Description: str
}
}
}
}
},
gnomad_age_hist_het: struct {
Description: str,
sub_annotations: struct {
bin_edges: struct {
Description: str
},
bin_freq: struct {
Description: str
},
n_smaller: struct {
Description: str
},
n_larger: struct {
Description: str
}
}
},
gnomad_age_hist_hom: struct {
Description: str,
sub_annotations: struct {
bin_edges: struct {
Description: str
},
bin_freq: struct {
Description: str
},
n_smaller: struct {
Description: str
},
n_larger: struct {
Description: str
}
}
},
filters: struct {
Description: str
},
info: struct {
Description: str,
sub_annotations: struct {
QUALapprox: struct {
Description: str
},
SB: struct {
Description: str
},
MQ: struct {
Description: str
},
MQRankSum: struct {
Description: str
},
VarDP: struct {
Description: str
},
AS_ReadPosRankSum: struct {
Description: str
},
AS_pab_max: struct {
Description: str
},
AS_QD: struct {
Description: str
},
AS_MQ: struct {
Description: str
},
QD: struct {
Description: str
},
AS_MQRankSum: struct {
Description: str
},
FS: struct {
Description: str
},
AS_FS: struct {
Description: str
},
ReadPosRankSum: struct {
Description: str
},
AS_QUALapprox: struct {
Description: str
},
AS_SB_TABLE: struct {
Description: str
},
AS_VarDP: struct {
Description: str
},
AS_SOR: struct {
Description: str
},
SOR: struct {
Description: str
},
transmitted_singleton: struct {
Description: str
},
omni: struct {
Description: str
},
mills: struct {
Description: str
},
monoallelic: struct {
Description: str
},
InbreedingCoeff: struct {
Description: str
}
}
},
vep: struct {
Description: str
},
vqsr: struct {
Description: str,
sub_annotations: struct {
AS_VQSLOD: struct {
Description: str
},
AS_culprit: struct {
Description: str
},
NEGATIVE_TRAIN_SITE: struct {
Description: str
},
POSITIVE_TRAIN_SITE: struct {
Description: str
}
}
},
region_flag: struct {
Description: str,
sub_annotations: struct {
lcr: struct {
Description: str
},
segdup: struct {
Description: str
}
}
},
allele_info: struct {
Description: str,
sub_annotations: struct {
variant_type: struct {
Description: str
},
allele_type: struct {
Description: str
},
n_alt_alleles: struct {
Description: str
}
}
},
was_mixed: struct {
Description: str
},
cadd: struct {
sub_annotations: struct {
raw_score: struct {
Description: str
},
phred: struct {
Description: str
},
has_duplicate: struct {
Description: str
}
}
},
revel: struct {
Description: str,
sub_annotations: struct {
revel_score: struct {
Description: str
},
has_duplicate: struct {
Description: str
}
}
},
splice_ai: struct {
sub_annotations: struct {
splice_ai: struct {
Description: str
},
splice_consequence: struct {
Description: str
},
has_duplicate: struct {
Description: str
}
}
},
primate_ai: struct {
sub_annotations: struct {
primate_ai_score: struct {
Description: str
},
has_duplicate: struct {
Description: str
}
}
},
AS_lowqual: struct {
Description: str
},
telomere_or_centromere: struct {
Description: str
}
}
'hgdp_tgp_freq_meta': array<dict<str, str>>
'hgdp_tgp_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
'variant_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>
}
'variant_inbreeding_coeff_cutoff': float64
----------------------------------------
Row fields:
'locus': locus<GRCh38>
'alleles': array<str>
'a_index': int32
'was_split': bool
'rsid': set<str>
'filters': set<str>
'info': struct {
SB: array<int32>,
MQRankSum: float64,
VarDP: int32,
AS_FS: float64,
AS_ReadPosRankSum: float64,
AS_pab_max: float64,
AS_QD: float32,
AS_MQ: float64,
AS_QUALapprox: int64,
QD: float32,
AS_MQRankSum: float64,
FS: float64,
MQ: float64,
ReadPosRankSum: float64,
QUALapprox: int64,
AS_SB_TABLE: array<int32>,
AS_VarDP: int32,
AS_SOR: float64,
SOR: float64,
transmitted_singleton: bool,
omni: bool,
mills: bool,
monoallelic: bool,
InbreedingCoeff: float32,
AS_VQSLOD: float64
}
'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
}
'hgdp_tgp_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_popmax': struct {
AC: int32,
AF: float64,
AN: int32,
homozygote_count: int32,
pop: str,
faf95: float64
}
'gnomad_faf': array<struct {
faf95: float64,
faf99: float64
}>
'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_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_age_hist_het': struct {
bin_edges: array<float64>,
bin_freq: array<int64>,
n_smaller: int64,
n_larger: int64
}
'gnomad_age_hist_hom': struct {
bin_edges: array<float64>,
bin_freq: array<int64>,
n_smaller: int64,
n_larger: int64
}
'cadd': struct {
phred: float32,
raw_score: float32,
has_duplicate: bool
}
'revel': struct {
revel_score: float64,
has_duplicate: bool
}
'splice_ai': struct {
splice_ai_score: float32,
splice_consequence: str,
has_duplicate: bool
}
'primate_ai': struct {
primate_ai_score: float32,
has_duplicate: bool
}
'AS_lowqual': bool
'telomere_or_centromere': bool
----------------------------------------
Key: ['locus', 'alleles']
----------------------------------------