[ensembl-dev] VEP: pheno data

[Andrew Parton]

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 <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> 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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