Vep runs successfully, but doesn't output CSQ even with csq=True

I’m running the script below on google cloud, but not seeing the CSQ field in the output vcf.

import hail

hc = hail.HailContext()

vds = (
hc.import_vcf(options.vcf, npartitions=1000)
 .annotate_variants_expr(' =[va.aIndex - 1], =[va.aIndex - 1]')
 .vep('/vep/', block_size=100, force=True, csq=True).cache()

print("COUNT", vds.count())


Only annotations located in are output to VCF. When running vep, the default annotation path is vds.vep and thus won’t be output.


Thanks! That fixed it.

.vep('/vep/', root='', block_size=100, force=True, csq=True)