[ensembl-dev] VEP: pheno data

[Nicolas Thierry-Mieg]

Thanks for your quick reply, and thanks for the link to the vep_formats 
page. It explains it all and I had forgotten about it somehow.

I was expecting things like DGVa / OMIM / other identifiers, not just a 
flag saying "this variant / gene is associated with a phenotype 
somewhere". But it's OK, now I know.

Regards,
Nicolas


On 03/26/2018 06:56 PM, Andrew Parton wrote:
> Hi Nicolas,
> 
> Thanks for your enquiry. This is expected behaviour, these flags return 
> the somatic status, whether the existing variant is associated with a 
> phenotype, or whether the overlapping gene is associated with a 
> phenotype. The symbol & is used to separate values if multiple existing 
> variants are found to overlap with the input data.
> 
> More information on these outputs can be found here: 
> https://www.ensembl.org/info/docs/tools/vep/vep_formats.html
> 
> If there’s anything else I can do to help, please let me know.
> 
> Kind Regards,
> Andrew Parton
> 
>> On 26 Mar 2018, at 17:10, Nicolas Thierry-Mieg 
>> <Nicolas.Thierry-Mieg at univ-grenoble-alpes.fr 
>> <mailto:Nicolas.Thierry-Mieg at univ-grenoble-alpes.fr>> wrote:
>>
>> Dear colleagues,
>>
>> I am running VEP latest (release/91), in offline mode with 
>> --gene_phenotype --check_existing .
>>
>> All I get in the SOMATIC, PHENO and GENE_PHENO columns are strings 
>> that look like boolean flags: "0&1" , "1", "0&1&1" ...
>>
>> I tried against both the default ENSEMBL cache and the refseq cache, 
>> with the same results.
>>
>> Full command-line:
>> vep --offline --vcf  --no_stats  --gene_phenotype  --check_existing 
>>  -i test.vcf -o test_vep.vcf
>>
>> Is this expected behavior, and if yes how do I interpret these values?
>> Otherwise, any suggestions? Re-install VEP from scratch? Clear and 
>> re-install the cache? Something else?
>>
>> Thanks.
>> Regards,
>> Nicolas
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> 
> 
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-- 
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Nicolas Thierry-Mieg
Laboratoire TIMC-IMAG/BCM, CNRS UMR 5525
Pavillon Taillefer, Faculte de Medecine
38700 La Tronche, France
tel: (+33)456.520.067, fax: (+33)456.520.055
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