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"reference_genome": "GRCh37",
},
)
syndip = MatrixTableResource(
path="gs://gnomad-public/resources/grch37/syndip/hybrid.m37m.mt",
import_func=hl.import_vcf,
import_args={
"path": "gs://gnomad-public/resources/grch37/syndip/hybrid.m37m.vcf.bgz",
"min_partitions": 100,
"reference_genome": "GRCh37",
},
)
# Versioned resources: versions should be listed from most recent to oldest
dbsnp = VersionedTableResource(
default_version="20180423",
versions={
"20180423": TableResource(
path="gs://gnomad-public/resources/grch37/dbsnp/All_20180423.ht",
import_func=import_sites_vcf,
import_args={
"path": "gs://gnomad-public/resources/grch37/dbsnp/All_20180423.vcf.bgz",
"force_bgz": True,
"skip_invalid_loci": True,
"min_partitions": 100,
"reference_genome": "GRCh37",
},
)
},
)
:param data_type: One of "exomes" or "genomes"
:return: Release Table
"""
if data_type not in DATA_TYPES:
raise DataException(f"{data_type} not in {DATA_TYPES}")
if data_type == "exomes":
current_release = CURRENT_EXOME_RELEASE
releases = EXOME_RELEASES
else:
current_release = CURRENT_GENOME_RELEASE
releases = GENOME_RELEASES
return VersionedTableResource(
current_release,
{
release: TableResource(path=_public_release_ht_path(data_type, release))
for release in releases
},
:param data_type: One of "exomes" or "genomes"
:return: Coverage Table
"""
if data_type not in DATA_TYPES:
raise DataException(f"{data_type} not in {DATA_TYPES}")
if data_type == "exomes":
current_release = "2.1"
releases = EXOME_RELEASES
releases.remove("2.1.1")
else:
current_release = CURRENT_GENOME_RELEASE
releases = GENOME_RELEASES
return VersionedTableResource(
current_release,
{
release: TableResource(path=_public_coverage_ht_path(data_type, release))
for release in releases
},
:param data_type: One of "exomes" or "genomes"
:return: Coverage Table
"""
if data_type not in DATA_TYPES:
raise DataException(
f"{data_type} not in {DATA_TYPES}, please select a data type from {DATA_TYPES}"
)
if data_type == "exomes":
current_release = CURRENT_EXOME_RELEASE
releases = EXOME_RELEASES
else:
current_release = CURRENT_GENOME_RELEASE
releases = GENOME_RELEASES
return VersionedTableResource(
current_release,
{
release: TableResource(path=_public_coverage_ht_path(data_type, release))
for release in releases
},
:return: Release Table
"""
if data_type not in DATA_TYPES:
raise DataException(
f"{data_type} not in {DATA_TYPES}, please select a data type from {DATA_TYPES}"
)
if data_type == "exomes":
current_release = CURRENT_EXOME_RELEASE
releases = EXOME_RELEASES
else:
current_release = CURRENT_GENOME_RELEASE
releases = GENOME_RELEASES
return VersionedTableResource(
current_release,
{
release: TableResource(path=_public_release_ht_path(data_type, release))
for release in releases
},
versions={
"20180423": TableResource(
path="gs://gnomad-public/resources/grch37/dbsnp/All_20180423.ht",
import_func=import_sites_vcf,
import_args={
"path": "gs://gnomad-public/resources/grch37/dbsnp/All_20180423.vcf.bgz",
"force_bgz": True,
"skip_invalid_loci": True,
"min_partitions": 100,
"reference_genome": "GRCh37",
},
)
},
)
clinvar = VersionedTableResource(
default_version="20181028",
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",
},
)
},
)
),
"phase_3": MatrixTableResource(
path="gs://gnomad-public/resources/grch37/kgp/1000Genomes_phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.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",
},
),
},
)
kgp = VersionedTableResource(
default_version="phase_1_hc",
versions={
"phase_1_hc": TableResource(
path="gs://gnomad-public/resources/grch37/kgp/1000G_phase1.snps.high_confidence.b37.ht",
import_func=import_sites_vcf,
import_args={
"path": "gs://gnomad-public/resources/grch37/kgp/1000G_phase1.snps.high_confidence.b37.vcf.bgz",
"force_bgz": True,
"skip_invalid_loci": True,
"min_partitions": 100,
"reference_genome": "GRCh37",
},
),
},
)
:param data_type: One of "exomes" or "genomes"
:return: Release Table
"""
if data_type not in DATA_TYPES:
raise DataException(f"{data_type} not in {DATA_TYPES}")
if data_type == "exomes":
current_release = CURRENT_EXOME_RELEASE
releases = EXOME_RELEASES
releases.remove("2.1")
else:
current_release = CURRENT_GENOME_RELEASE
releases = GENOME_RELEASES
return VersionedTableResource(
current_release,
{
release: TableResource(path=_liftover_data_path(data_type, release))
for release in releases
},