def _import_clinvar(**kwargs) -> hl.Table:
clinvar = import_sites_vcf(**kwargs)
clinvar = clinvar.filter(
hl.len(clinvar.alleles) > 1
) # Get around problematic single entry in alleles array in the clinvar vcf
clinvar = vep_or_lookup_vep(clinvar, reference="GRCh38")
return clinvar
def _import_dbsnp(**kwargs) -> hl.Table:
dbsnp = import_sites_vcf(**kwargs)
# Note: permit_shuffle is set because the dbsnp vcf has duplicate loci (turned into a set) so might be out of order
dbsnp = hl.split_multi(dbsnp, permit_shuffle=True)
dbsnp = dbsnp.group_by(
dbsnp.locus,
dbsnp.alleles).aggregate(rsid=hl.agg.collect_as_set(dbsnp.rsid))
return dbsnp