I'm using the Ensembl Variant Effect Predictor (VEP) to annotate VCF files, and I am trying to add some additional fields to the output, among these is
OVERLAP_BP, which is listed here in available fields:
OVERLAP_BP - Number of base pairs overlapping with the corresponding variation feature
It's clear that some (many? all?) of these additional fields are only enabled by adding extra options to the VEP command (as listed on the RHS of the options table).
For example, the
ZYG field is made available by adding the
--individual flag to the VEP call.
OVERLAP_BP doesn’t appear in the output fields column on that page, and when I add it to the output using
--fields, it is consistently empty.
What options are required to make the
OVERLAP_BP output field available to me in VEP?