[ensembl-dev] Output format

[Jennifer Yen]

Hi Ensembl Team,

Is there a flag for including the original vcf position and allele in the
vep output? For indels the output positions change (specified over a range,
rather than the start position in the vcf) and the reference allele is
never in the output.  This would be useful for cross-referencing with
different files using the positions as identifiers in the vcf.

Thanks,
Jenn

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