[ensembl-dev] VEP ignoring --fasta option

[Ivan Adzhubey]

Hi Will,

Thank you for your prompt reply. Please scroll down for my comment.

On Monday, April 11, 2016 10:44:38 AM Will McLaren wrote:
> Hi Ivan,
> 
> The VEP will auto-detect a FASTA file in your cache directory, which is
> presumably what is being used when you specify --everything without --fasta.

May I suggest documenting it properly? It took me three days to debug the 
program crashes due to this non-documented FASTA auto-detection feature.

> There's currently no way to disable this auto-detection; the easiest thing
> to do would be to remove or move the file (typically
> $HOME/.vep/homo_sapiens/84_GRCh38/*.fa)

Yes that's exactly what I did. But such workaround prevents other users from 
annotating sequence features, so this is not a good solution (our installation 
is on a shared cluster).

> You could alternately manually list the options set by --everything,
> excluding --hgvs as this is what uses the sequence lookups.

Still, I would really prefer if VEP would require explicit --fasta option in 
order to enable FASTA files auto-detection.

Thanks,
Ivan


-- 
Ivan Adzhubey, Ph.D.
Instructor
Division of Genetics, Dept of Medicine
Brigham & Women's Hospital
Harvard Medical School
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