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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",
},
),
},
)
cpg_sites = TableResource(path="gs://gnomad-public/resources/grch37/cpg_sites/cpg.ht")
methylation_sites = TableResource(
import_args={
"path": "gs://gnomad-public/resources/grch37/decoy_intervals/mm-2-merged.GRCh37_compliant.bed",
"reference_genome": "GRCh37",
},
)
purcell_5k_intervals = TableResource(
path="gs://gnomad-public/resources/grch37/purcell_5k_intervals/purcell5k.ht",
import_func=hl.import_locus_intervals,
import_args={
"path": "gs://gnomad-public/resources/grch37/purcell_5k_intervals/purcell5k.interval_list",
"reference_genome": "GRCh37",
},
)
seg_dup_intervals = TableResource(
path="gs://gnomad-public/resources/grch37/seg_dup_intervals/hg19_self_chain_split_both.ht",
import_func=hl.import_bed,
import_args={
"path": "gs://gnomad-public/resources/grch37/seg_dup_intervals/hg19_self_chain_split_both.bed",
"reference_genome": "GRCh37",
},
)
exome_hc_intervals = TableResource(
path="gs://gnomad-public/resources/grch37/broad_intervals/exomes_high_coverage.auto.interval_list.ht",
import_func=hl.import_locus_intervals,
import_args={
"path": "gs://gnomad-public/resources/grch37/broad_intervals/exomes_high_coverage.auto.interval_list",
"reference_genome": "GRCh37",
},
)
"reference_genome": "GRCh37",
},
)
kgp_omni = TableResource(
path="gs://gnomad-public/resources/grch37/kgp/1000G_omni2.5.b37.ht",
import_func=import_sites_vcf,
import_args={
"path": "gs://gnomad-public/resources/grch37/kgp/1000G_omni2.5.b37.vcf.bgz",
"force_bgz": True,
"min_partitions": 100,
"reference_genome": "GRCh37",
},
)
mills = TableResource(
path="gs://gnomad-public/resources/grch37/mills/Mills_and_1000G_gold_standard.indels.b37.ht",
import_func=import_sites_vcf,
import_args={
"path": "gs://gnomad-public/resources/grch37/mills/Mills_and_1000G_gold_standard.indels.b37.vcf.bgz",
"force_bgz": True,
"min_partitions": 100,
"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,
def ld_index(pop: str) -> TableResource:
return TableResource(path=_ld_index_path("genomes", pop))
"""
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
},
def ld_scores(pop: str) -> TableResource:
return TableResource(path=_ld_scores_path("genomes", pop))
"""
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
},
import_args={
"path": "gs://gnomad-public/resources/grch37/broad_intervals/hg19-v0-wgs_evaluation_regions.v1.interval_list",
"reference_genome": "GRCh37",
},
)
na12878_hc_intervals = TableResource(
path="gs://gnomad-public/resources/grch37/na12878/NA12878_GIAB_highconf_intervals.ht",
import_func=hl.import_bed,
import_args={
"path": "gs://gnomad-public/resources/grch37/na12878/NA12878_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-Solid-10X_CHROM1-X_v3.3_highconf.bed",
"reference_genome": "GRCh37",
},
)
syndip_hc_intervals = TableResource(
path="gs://gnomad-public/resources/grch37/syndip/syndip_highconf_genome_intervals.ht",
import_func=hl.import_bed,
import_args={
"path": "gs://gnomad-public/resources/grch37/syndip/hybrid.m37m.bed",
"reference_genome": "GRCh37",
},
)
def get_truth_ht() -> hl.Table:
"""
Returns a table with the following annotations from the latest version of the corresponding truth data:
- hapmap
- kgp_omni (1000 Genomes intersection Onni 2.5M array)
- kgp_phase_1_hc (high confidence sites in 1000 genonmes)
- mills (Mills & Devine indels)
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
},
"force_bgz": True,
"skip_invalid_loci": True,
"min_partitions": 100,
"reference_genome": "GRCh37",
},
),
},
)
cpg_sites = TableResource(path="gs://gnomad-public/resources/grch37/cpg_sites/cpg.ht")
methylation_sites = TableResource(
path="gs://gnomad-public/resources/grch37/methylation_sites/methylation.ht"
)
lcr_intervals = TableResource(
path="gs://gnomad-public/resources/grch37/lcr_intervals/LCR.GRCh37_compliant.interval_list.ht",
import_func=hl.import_locus_intervals,
import_args={
"path": "gs://gnomad-public/resources/grch37/lcr_intervals/LCR.GRCh37_compliant.interval_list",
"reference_genome": "GRCh37",
},
)
decoy_intervals = TableResource(
path="gs://gnomad-public/resources/grch37/decoy_intervals/mm-2-merged.GRCh37_compliant.ht",
import_func=hl.import_bed,
import_args={
"path": "gs://gnomad-public/resources/grch37/decoy_intervals/mm-2-merged.GRCh37_compliant.bed",
"reference_genome": "GRCh37",
},
)