[ensembl-dev] VEP - feature request - VCF output file as an additional output file

Duarte Molha Duarte.Molha at ogt.co.uk
Thu May 10 17:27:48 BST 2012


I am having fun with the latest VEP. Thank you for the hard work!

However I would like to make a feature request... Could you make the  -VCF behaviour different?

It would be great if the script could output the annotation in regular tab delimited format and the -VCF flag could be used to specify a additional output filename for the same data in VCF format.

The VCF format is very useful and portable but for some things but it would be a headache to parse the variant annotations from the info field so it would be great it from 1 run we could get both files.

Cheers,
Duarte Molha

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