gnomad_hgdp_1kg_subset_dense
Versions: 3.1, 3.1.2
Reference genome builds: GRCh38
Type:
hail.MatrixTable
Schema (3.1.2, GRCh38)
----------------------------------------
Global fields:
'global_annotation_descriptions': struct {
gnomad_sex_imputation_ploidy_cutoffs: struct {
Description: str
},
gnomad_population_inference_pca_metrics: struct {
Description: str
},
sample_hard_filter_cutoffs: struct {
Description: str
},
gnomad_sample_qc_metric_outlier_cutoffs: struct {
Description: str
},
gnomad_age_distribution: struct {
Description: str,
sub_globals: struct {
bin_edges: struct {
Description: str
},
bin_freq: struct {
Description: str
},
n_smaller: struct {
Description: str
},
n_larger: struct {
Description: str
}
}
},
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
}
}
'sample_annotation_descriptions': struct {
s: struct {
Description: str
},
bam_metrics: struct {
Description: str,
sub_annotations: struct {
pct_bases_20x: struct {
Description: str
},
pct_chimeras: struct {
Description: str
},
freemix: struct {
Description: str
},
mean_coverage: struct {
Description: str
},
median_coverage: struct {
Description: str
},
mean_insert_size: struct {
Description: str
},
median_insert_size: struct {
Description: str
},
pct_bases_10x: struct {
Description: str
}
}
},
sample_qc: struct {
Description: str,
sub_annotations: struct {
n_deletion: struct {
Description: str
},
n_het: struct {
Description: str
},
n_hom_ref: struct {
Description: str
},
n_hom_var: struct {
Description: str
},
n_insertion: struct {
Description: str
},
n_non_ref: struct {
Description: str
},
n_snp: struct {
Description: str
},
n_transition: struct {
Description: str
},
n_transversion: struct {
Description: str
},
r_het_hom_var: struct {
Description: str
},
r_insertion_deletion: struct {
Description: str
},
r_ti_tv: struct {
Description: str
}
}
},
gnomad_sex_imputation: struct {
Description: str,
sub_annotations: struct {
chr20_mean_dp: struct {
Description: str
},
chrX_mean_dp: struct {
Description: str
},
chrY_mean_dp: struct {
Description: str
},
chrX_ploidy: struct {
Description: str
},
chrY_ploidy: struct {
Description: str
},
X_karyotype: struct {
Description: str
},
Y_karyotype: struct {
Description: str
},
sex_karyotype: struct {
Description: str
},
f_stat: struct {
Description: str
},
n_called: struct {
Description: str
},
expected_homs: struct {
Description: str
},
observed_homs: struct {
Description: str
}
}
},
gnomad_population_inference: struct {
Description: str,
sub_annotations: struct {
pca_scores: struct {
Description: str
},
pop: struct {
Description: str
},
prob_afr: struct {
Description: str
},
prob_ami: struct {
Description: str
},
prob_amr: struct {
Description: str
},
prob_asj: struct {
Description: str
},
prob_eas: struct {
Description: str
},
prob_fin: struct {
Description: str
},
prob_mid: struct {
Description: str
},
prob_nfe: struct {
Description: str
},
prob_oth: struct {
Description: str
},
prob_sas: struct {
Description: str
}
}
},
gnomad_sample_qc_residuals: struct {
Description: tuple (
str
),
sub_annotations: struct {
n_snp_residual: struct {
Description: str
},
r_ti_tv_residual: struct {
Description: str
},
r_insertion_deletion_residual: struct {
Description: str
},
n_insertion_residual: struct {
Description: str
},
n_deletion_residual: struct {
Description: str
},
r_het_hom_var_residual: struct {
Description: str
},
n_transition_residual: struct {
Description: str
},
n_transversion_residual: struct {
Description: str
}
}
},
gnomad_sample_filters: struct {
Description: str,
sub_annotations: struct {
hard_filters: struct {
Description: str
},
hard_filtered: struct {
Description: str
},
release_related: struct {
Description: str
},
qc_metrics_filters: struct {
Description: str
}
}
},
gnomad_high_quality: struct {
Description: str
},
gnomad_release: struct {
Description: str
},
relatedness_inference: struct {
Description: str,
sub_annotations: struct {
related_samples: struct {
Description: str,
sub_annotations: struct {
s: struct {
Description: str
},
kin: struct {
Description: str
},
ibd0: struct {
Description: str
},
ibd1: struct {
Description: str
},
ibd2: struct {
Description: str
}
}
},
related: struct {
Description: str
}
}
},
hgdp_tgp_meta: struct {
Description: str,
sub_annotations: struct {
project: struct {
Description: str
},
study_region: struct {
Description: str
},
population: struct {
Description: str
},
genetic_region: struct {
Description: str
},
latitude: struct {
Description: str
},
longitude: struct {
Description: str
},
hgdp_technical_meta: struct {
Description: str,
sub_annotations: struct {
source: struct {
Description: str
},
library_type: struct {
Description: str
}
}
},
global_pca_scores: struct {
Description: str
},
subcontinental_pca: struct {
Description: str,
sub_annotations: struct {
pca_scores: struct {
Description: str
},
pca_scores_outliers_removed: struct {
Description: str
},
outlier: struct {
Description: str
}
}
},
gnomad_labeled_subpop: struct {
Description: str
}
}
},
high_quality: struct {
Description: str
}
}
'gnomad_sex_imputation_ploidy_cutoffs': struct {
x_ploidy_cutoffs: struct {
upper_cutoff_X: float64,
lower_cutoff_XX: float64,
upper_cutoff_XX: float64,
lower_cutoff_XXX: float64
},
y_ploidy_cutoffs: struct {
lower_cutoff_Y: float64,
upper_cutoff_Y: float64,
lower_cutoff_YY: float64
},
f_stat_cutoff: float64
}
'gnomad_population_inference_pca_metrics': struct {
n_pcs: int32,
min_prob: float64
}
'sample_hard_filter_cutoffs': struct {
min_cov: int32,
max_n_snp: float64,
min_n_snp: float64,
max_n_singleton: float64,
max_r_het_hom_var: float64,
max_pct_contamination: float64,
max_pct_chimera: float64,
min_median_insert_size: int32
}
'gnomad_sample_qc_metric_outlier_cutoffs': struct {
lms: struct {
n_snp: struct {
beta: array<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
multiple_standard_error: float64,
multiple_r_squared: float64,
adjusted_r_squared: float64,
f_stat: float64,
multiple_p_value: float64,
n: int32
},
n_singleton: struct {
beta: array<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
multiple_standard_error: float64,
multiple_r_squared: float64,
adjusted_r_squared: float64,
f_stat: float64,
multiple_p_value: float64,
n: int32
},
r_ti_tv: struct {
beta: array<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
multiple_standard_error: float64,
multiple_r_squared: float64,
adjusted_r_squared: float64,
f_stat: float64,
multiple_p_value: float64,
n: int32
},
r_insertion_deletion: struct {
beta: array<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
multiple_standard_error: float64,
multiple_r_squared: float64,
adjusted_r_squared: float64,
f_stat: float64,
multiple_p_value: float64,
n: int32
},
n_insertion: struct {
beta: array<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
multiple_standard_error: float64,
multiple_r_squared: float64,
adjusted_r_squared: float64,
f_stat: float64,
multiple_p_value: float64,
n: int32
},
n_deletion: struct {
beta: array<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
multiple_standard_error: float64,
multiple_r_squared: float64,
adjusted_r_squared: float64,
f_stat: float64,
multiple_p_value: float64,
n: int32
},
r_het_hom_var: struct {
beta: array<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
multiple_standard_error: float64,
multiple_r_squared: float64,
adjusted_r_squared: float64,
f_stat: float64,
multiple_p_value: float64,
n: int32
},
n_transition: struct {
beta: array<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
multiple_standard_error: float64,
multiple_r_squared: float64,
adjusted_r_squared: float64,
f_stat: float64,
multiple_p_value: float64,
n: int32
},
n_transversion: struct {
beta: array<float64>,
standard_error: array<float64>,
t_stat: array<float64>,
p_value: array<float64>,
multiple_standard_error: float64,
multiple_r_squared: float64,
adjusted_r_squared: float64,
f_stat: float64,
multiple_p_value: float64,
n: int32
}
},
qc_metrics_stats: struct {
n_snp_residual: struct {
median: float64,
mad: float64,
lower: float64,
upper: float64
},
n_singleton_residual: struct {
median: float64,
mad: float64,
lower: float64,
upper: float64
},
r_ti_tv_residual: struct {
median: float64,
mad: float64,
lower: float64,
upper: float64
},
r_insertion_deletion_residual: struct {
median: float64,
mad: float64,
lower: float64,
upper: float64
},
n_insertion_residual: struct {
median: float64,
mad: float64,
lower: float64,
upper: float64
},
n_deletion_residual: struct {
median: float64,
mad: float64,
lower: float64,
upper: float64
},
r_het_hom_var_residual: struct {
median: float64,
mad: float64,
lower: float64,
upper: float64
},
n_transition_residual: struct {
median: float64,
mad: float64,
lower: float64,
upper: float64
},
n_transversion_residual: struct {
median: float64,
mad: float64,
lower: float64,
upper: float64
}
},
n_pcs: int32,
used_regressed_metrics: bool
}
'gnomad_age_distribution': struct {
bin_edges: array<float64>,
bin_freq: array<int32>,
n_smaller: int32,
n_larger: int32
}
'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
----------------------------------------
Column fields:
's': str
'bam_metrics': struct {
pct_bases_20x: float64,
pct_chimeras: float64,
freemix: float64,
mean_coverage: float64,
median_coverage: float64,
mean_insert_size: float64,
median_insert_size: float64,
pct_bases_10x: float64
}
'sample_qc': struct {
n_deletion: int64,
n_het: int64,
n_hom_ref: int64,
n_hom_var: int64,
n_insertion: int64,
n_non_ref: int64,
n_snp: int64,
n_transition: int64,
n_transversion: int64,
r_het_hom_var: float64,
r_insertion_deletion: float64,
r_ti_tv: float64
}
'gnomad_sex_imputation': struct {
chr20_mean_dp: float32,
chrX_mean_dp: float32,
chrY_mean_dp: float32,
chrX_ploidy: float32,
chrY_ploidy: float32,
X_karyotype: str,
Y_karyotype: str,
sex_karyotype: str,
f_stat: float64,
n_called: int64,
expected_homs: float64,
observed_homs: int64
}
'gnomad_population_inference': struct {
pca_scores: array<float64>,
pop: str,
prob_afr: float64,
prob_ami: float64,
prob_amr: float64,
prob_asj: float64,
prob_eas: float64,
prob_fin: float64,
prob_mid: float64,
prob_nfe: float64,
prob_oth: float64,
prob_sas: float64
}
'gnomad_sample_qc_residuals': struct {
n_snp_residual: float64,
r_ti_tv_residual: float64,
r_insertion_deletion_residual: float64,
n_insertion_residual: float64,
n_deletion_residual: float64,
r_het_hom_var_residual: float64,
n_transition_residual: float64,
n_transversion_residual: float64
}
'gnomad_sample_filters': struct {
hard_filters: set<str>,
hard_filtered: bool,
release_related: bool,
qc_metrics_filters: set<str>
}
'gnomad_high_quality': bool
'gnomad_release': bool
'relatedness_inference': struct {
related_samples: set<struct {
s: str,
kin: float64,
ibd0: float64,
ibd1: float64,
ibd2: float64
}>,
related: bool
}
'hgdp_tgp_meta': struct {
project: str,
study_region: str,
population: str,
genetic_region: str,
latitude: float64,
longitude: float64,
hgdp_technical_meta: struct {
source: str,
library_type: str
},
global_pca_scores: array<float64>,
subcontinental_pca: struct {
pca_scores: array<float64>,
pca_scores_outliers_removed: array<float64>,
outlier: bool
},
gnomad_labeled_subpop: str
}
'high_quality': bool
----------------------------------------
Row fields:
'locus': locus<GRCh38>
'alleles': array<str>
'rsid': set<str>
'a_index': int32
'was_split': bool
'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
}
----------------------------------------
Entry fields:
'DP': int32
'GQ': int32
'MIN_DP': int32
'PID': str
'RGQ': int32
'SB': array<int32>
'GT': call
'PGT': call
'AD': array<int32>
'PL': array<int32>
'adj': bool
----------------------------------------
Column key: ['s']
Row key: ['locus', 'alleles']
----------------------------------------