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

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1

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)
 .split_multi()
 .annotate_variants_expr('va.info.AC = va.info.AC[va.aIndex - 1], va.info.AF = va.info.AF[va.aIndex - 1]')
 .vep('/vep/vep-gcloud.properties', block_size=100, force=True, csq=True).cache()
)

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

vds.export_vcf(output_vcf)
2

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

Cheers,
Laurent

3

Thanks! That fixed it.

.vep('/vep/vep-gcloud.properties', root='va.info.CSQ', block_size=100, force=True, csq=True)