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VersionedMatrixTableResource,
MatrixTableResource,
VersionedTableResource,
DataException,
)
from typing import Optional
CURRENT_EXOME_RELEASE = ""
CURRENT_GENOME_RELEASE = "3.0"
EXOME_RELEASES = []
GENOME_RELEASES = ["3.0"]
DATA_TYPES = ["genomes"]
GENOME_POPS = ["AFR", "AMI", "AMR", "ASJ", "EAS", "FIN", "NFE", "SAS", "OTH"]
gnomad_syndip = VersionedMatrixTableResource(
default_version="3.0",
versions={
"3.0": MatrixTableResource(
path="gs://gnomad-public/truth-sets/hail-0.2/gnomad_v3_syndip.b38.mt"
)
},
)
na12878 = VersionedMatrixTableResource(
default_version="3.0",
versions={
"3.0": MatrixTableResource(
path="gs://gnomad-public/truth-sets/hail-0.2/gnomad_v3_na12878.mt"
)
},
)
EXOME_RELEASES = []
GENOME_RELEASES = ["3.0"]
DATA_TYPES = ["genomes"]
GENOME_POPS = ["AFR", "AMI", "AMR", "ASJ", "EAS", "FIN", "NFE", "SAS", "OTH"]
gnomad_syndip = VersionedMatrixTableResource(
default_version="3.0",
versions={
"3.0": MatrixTableResource(
path="gs://gnomad-public/truth-sets/hail-0.2/gnomad_v3_syndip.b38.mt"
)
},
)
na12878 = VersionedMatrixTableResource(
default_version="3.0",
versions={
"3.0": MatrixTableResource(
path="gs://gnomad-public/truth-sets/hail-0.2/gnomad_v3_na12878.mt"
)
},
)
def _public_release_ht_path(data_type: str, version: str) -> str:
"""
Get public release table path
:param data_type: One of "exomes" or "genomes"
:param version: One of the release versions of gnomAD on GRCh38
:return: Path to release Table
versions={
"20181028": TableResource(
path="gs://gnomad-public/resources/grch37/clinvar/clinvar_20181028.vep.ht",
import_func=import_sites_vcf,
import_args={
"path": "gs://gnomad-public/resources/grch37/clinvar/clinvar_20181028.vcf.bgz",
"force_bgz": True,
"skip_invalid_loci": True,
"min_partitions": 100,
"reference_genome": "GRCh37",
},
)
},
)
kgp_phase_3 = VersionedMatrixTableResource(
default_version="phase_3_split",
versions={
"phase_3_split": MatrixTableResource(
path="gs://gnomad-public/resources/grch37/kgp/1000Genomes_phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.split.mt",
import_func=hl.import_vcf,
import_args={
"path": "gs://genomics-public-data/1000-genomes-phase-3/vcf-20150220/ALL.chr*.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf",
"force_bgz": True,
"skip_invalid_loci": True,
"min_partitions": 300,
"reference_genome": "GRCh37",
},
),
"phase_3": MatrixTableResource(
path="gs://gnomad-public/resources/grch37/kgp/1000Genomes_phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.mt",
import_func=hl.import_vcf,