I got a VCF from an individual that shows symptoms of a known disease with known mutations. I run it with Ensembl-vep, expecting to find some of those mutations in the results, yet, all the consequences in the results are "intergenic-variant".
The command I used was:
--cache --input_file sample.vcf
According to the VEP summary, the annotation source was:
Cache: /.vep/homo_sapiens/106_GRCh38; homo_sapiens_core_106_38 on ensembldb.ensembl.org
Any ideas why I got this results instead of the expected annotations? From your experience, could the Ensembl-vep result be wrong as a result of the command I used (the VCF file is ok)?