[ensembl-dev] Help with VEP options

Paila, Uma Devi (udp3f) udp3f at eservices.virginia.edu
Wed Feb 1 17:44:54 GMT 2012

Hi developers of VEP,

It was great using the latest version of your tool  (v2.3) 'Variant effect Predictor'  which looks promising. We were actually interested in the standalone version of your software but encountered some issues when trying to use the script with the —cache option on mac. There was some issue with the reading of the transcript data  in the cache, though gzip and zcat utilities were installed on the local machine (basically a mac environment and not linux). The errors that I get are:

~/.vep/homo_sapiens/65/1/1-1000000.gz.Z: No such file or directory

Magic number checking on storable file failed

We were wondering if that could be fixed by some means. It would be a great help!

Secondly, if we understand correctly, the –sift and –polyphen options were lately introduced and are not in terms with the –vcf option. It would have been great if we could see the polyphen and sift predictions under 'CSQ' of an output vcf file, when we choose the three output options as;
--sift —polyphen —vcf
We understand it has been clearly documented that the –vcf option only displays consequence type, but it would be of great use if the —vcf option was available in conjugation with the —sift and —polyphen options. Please let us know if you could make that option available to us.


Uma D.Paila (Ph.D),
Research Associate with Dr. Aaron Quinlan,
Center for Public Health Genomics,
University of Virginia, VA
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