[ensembl-dev] Fwd: how to include info from VCF file in VEP output

Will McLaren wm2 at ebi.ac.uk
Fri Mar 2 14:27:07 GMT 2012


Hi Denis,

Using the latest version of the VEP script (v2.4 and the Ensembl API
v66) you can get comprehensive VCF output from the VEP - you use the
--vcf flag.

This means you can use a VCF as the input file, and the output will be
your original VCF file with the consequence information added under
the "CSQ" key in the VCF's INFO column. Any frequency or other
information in the INFO column will be preserved.

You could also (with a bit of trickery) use the custom annotation
function of the VEP
(http://www.ensembl.org/info/docs/variation/vep/vep_script.html#custom)
to add the same information to the default VEP output format.

If you are using the web version of the VEP neither of these are
currently possible; I would suggest writing a simple perl or python
script to copy the data, or use something like vcf-annotate
(http://vcftools.sourceforge.net/perl_module.html#vcf-annotate).

Hope this helps!

Cheers

Will McLaren
Ensembl Variation

On 2 March 2012 14:18, Denis Reshetov <reshetovdenis at rogaevlab.ru> wrote:
> Dear colleagues, I'd like to add some info like AF from original
> vcf file to the output of VEP. Is there a simple way to do it?
>
> Kind regards,
>
> --
> Denis Reshetov
> PhD Student
> Dr. Rogaev Laboratory, Moscow,
> Vavilov Institute of General Genetics
> tel.: +7-917-523-26-84
> skype: reshetovdenis1
>
> CC
> Dr. Rogaev, PhD, Dr.Sci.,
> Professor of Psychiatry, University of Massachusetts Medical School, Worcester,
> BNRI, 303 Belmont Street, USA, MA 01604
> (508)8568493 lab
> (508)8568438 office
> Head, Dep of Human Genetics and Genomics,
> Vavilov Institute of General Genetics
>
>
> --
> Denis Reshetov
> PhD Student
> Dr. Rogaev Laboratory, Moscow,
> Vavilov Institute of General Genetics
> tel.: +7-917-523-26-84
> skype: reshetovdenis1
>
> CC
> Dr. Rogaev, PhD, Dr.Sci.,
> Professor of Psychiatry, University of Massachusetts Medical School, Worcester,
> BNRI, 303 Belmont Street, USA, MA 01604
> (508)8568493 lab
> (508)8568438 office
> Head, Dep of Human Genetics and Genomics,
> Vavilov Institute of General Genetics
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/




More information about the Dev mailing list