[ensembl-dev] VEP: Perform lift over

Sarah Hunt seh at ebi.ac.uk
Thu Apr 9 09:27:00 BST 2020

Hi Margaret,

VEP focuses on variant annotation and doesn't perform lift overs. We 
have an Assembly Converter web tool you may find useful:


As you will see, this uses the Crossmap package, which you could install 
locally if you are looking for a command line option.

Best wishes,


On 08/04/2020 17:59, Linan, Margaret wrote:
> Hi,
> Can I get a example script for using command line VEP to convert a 
> hg19 VCF file to a VCF with GRCh38 coordinates?
> Also is it possible to include the coordinates from hg19 in the GRCh38 
> lifted VCF file?
> Best,
> Margaret
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