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

[Will McLaren]

Hi Denis,

The VEP does in fact do these things - you need to update to the
latest version (released only this week, so you may have missed it).

http://www.ensembl.org/info/docs/variation/vep/vep_script.html#new

http://www.ensembl.org/info/docs/variation/vep/vep_script.html#download

Thanks

Will

On 2 March 2012 18:24, Denis Reshetov <reshetovdenis at rogaevlab.ru> wrote:
> Thanks Will,
> unfortunately --vcf flag produce vcf file with no annotation of transcript,
> gene name and Polyphen info.
> It would be great if VEP could add annotation to vcf file like it does
> GATK with SnpEff.
> I used this pipeline but I encountered serious problems with quality
> of annotation.
> VEP quality looks quite good.
>
> Kind regards,
> Denis
>
> 2012/3/2 Will McLaren <wm2 at ebi.ac.uk>:
>> 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/
>>
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>
>
>
> --
> 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/