[ensembl-dev] VEP API and parsing multiallelic variants

[Joseph A Prinz]

Hi ensembl devs!

I am writing a plugin for VEP that will process a VCF file using the BaseVepTabixPlugin class.
My goal is to be able to match alleles between the output of VEP and the overlapping portions of the VCF file being processed by the plugin.

To this end, I have been using the ExAC plugin as a rough guide, and have am using Utils::VEP parse_line to parse the tabix results.
I have noticed that parse_line will not try to minimize variants that are multiallelic (this case is excluded by minimize_variants called by parse_line).
The private method split_variants looks like what I am looking for, but the only public method evoking it is get_all_consequences and this may be cumbersome for a large VCF file.

What would be the most efficient way to leverage the API to transform alleles of a VCF to be comparable with those being produced by VEP?
Also, would you consider adding split_variants as an optional parameter to parse_line?

Thank you!
Joey