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

[Denis Reshetov]

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
>>
>> _______________________________________________
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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