Hi Valerie,

thanks a lot for looking following up on this issue.
Yes, I generated the input for ensemblVEP with a call to writeVcf.

Here's my workflow:

1. Variant calling with the '*callVariants*' function from the '*
VariantTools*' package: returns the* 'variants.gr' GRanges object*
2. Generate a Vcf object from the 'variant' GRanges with a call to '*
variantGR2Vcf'*: returns *variants.vcf VCF object*
3. write Vcf object to disk as a vcf file with '*writeVcf*': generates
variants.vcf file

You can find the variants.gr and variants.vcf R objects here:
https://dl.dropboxusercontent.com/u/126180/variants.object.Rdata
and the exported vcf file from the same data here:
https://dl.dropboxusercontent.com/u/126180/variants.vcf

Thanks a lot !
Thomas

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