def get_eigen(partitions : int = None,namenode : str = ""):
ht = import_vcf(
"hdfs://" + namenode + "/user/hdfs/data/EIGEN_coding_noncoding.grch37.vcf.gz",
"37",
"eigen",
min_partitions=partitions,
force_bgz=True)
return ht
def get_exac(partitions: int = None, namenode: str = ""):
ht = import_vcf("hdfs://" + namenode +
"/user/hdfs/data/ExAC.r1.sites.vep.vcf.gz",
"37",
"exac",
min_partitions=partitions,
force_bgz=True)
return ht
def get_mpc():
ht = import_vcf(
's3://seqr-resources/mpc/fordist_constraint_official_mpc_values.vcf.gz',
"37",
"mpc",
min_partitions=30
) #ht = import_vcf("s3://seqr-resources/topmed/bravo-dbsnp-all.removed_chr_prefix.liftunder_GRCh37.vcf.gz","37","topmed")
return ht
def load_hgmd_vcf(partitions: int = None, namenode: str = ""):
mt = import_vcf('hdfs://' + namenode +
'/user/hadoop/data/hgmd_pro_2018.4_hg19.vcf.gz',
"37",
"hgmd_grch37",
min_partitions=partitions,
force_bgz=True)
return mt
def get_topmed(partitions: int = None, namenode: str = ""):
ht = import_vcf(
"hdfs://" + namenode +
"/user/hdfs/data/bravo-dbsnp-all.removed_chr_prefix.liftunder_GRCh37.vcf.gz",
"37",
"topmed",
min_partitions=partitions,
force_bgz=True)
return ht
def import_primate(partitions : int = None,namenode : str = ""):
ht = import_vcf(
"hdfs://" + namenode + "/user/hdfs/data/PrimateAI_scores_v0.2.vcf.gz",
"37",
"primate_ai",
min_partitions=partitions,
force_bgz=True
)
return ht
def add_vcf_to_hail(sample: SeqrSample,
filename,
local=False,
genome_version="37",
partitions: int = None):
mt = import_vcf(filename,
genome_version,
sample.individual_id,
force_bgz=True,
min_partitions=partitions)
mt = add_global_metadata(mt, sample.path_to_vcf, sample.family_id,
sample.individual_id)
return mt