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.
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