[ensembl-dev] VEP: pheno data

[Nicolas Thierry-Mieg]

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