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

[Will McLaren]

Hi Denis,

Yes, this is a consequence of the "--most_severe" option. Since the
most severe consequence may occur in multiple transcripts, the
transcript information is omitted.

You may find the "--per_gene" flag more useful - this gives you one
consequence per gene, choosing the transcript that gives the most
severe consequence. However, for some variants you may still get more
than one consequence as it may overlap more than one gene.

Unfortunately, biology doesn't make it as simple as "the consequence"!

Will

On 3 March 2012 06:52, Denis Reshetov <reshetovdenis at rogaevlab.ru> wrote:
> Hi Will, I use the version you've mentioned. The problem
> is that when I switch on the "--most_severe" option
>  VEP stops to print info about transcripts.
>
> Many thanks,
> Denis
>
> 2012/3/2 Will McLaren <wm2 at ebi.ac.uk>:
>> 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
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>>>>> 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/
>>
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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/