Handling Intergenic Variants in the MAF: Annotation Pipeline doesn't fill out any columns when VEP returns no transcript

[rmadupuri]

When VEP doesnt return any transcript info (for intergenic variants), the annotation pipeline doesnt fill out any columns.
For example, https://www.genomenexus.org/annotation/2%3Ag.159740254C%3EA?fields=annotation_summary is an intergenic variant and this would get imported as MUTATED into the database although this is an intergenic event and should be filtered out. Importer uses Variant_Classification column to filter out the variants.

Solution:
Would be ideal to use the "most_severe_consequence" to update the Consequence (intergenic_variant) and Variant_Classification (IGR) coulumns so these would be filtered out during import.

More examples:
error.txt