[ensembl-dev] VCF input in VEP

[Genomeo Dev]

Hi,

The following documentation shows that ensembl use a customised VCF format
at least for VEP which is different to the original VCF used by 1000
genomes:

http://www.ensembl.org/info/docs/tools/vep/vep_formats.html

This difference seems to affect only balanced variations.

I am working with data straight from 1000 genomes which I want to process
with VEP. Many of them don't have assigned dbSNP IDs so can't run VEP with
ID as input. Would it be possible for Ensembl to share their script for
converting the original VCFs to their customised VCF?

P.S. Using VM 74 and VEP 74.

Thanks,

G.
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