[ensembl-dev] VEP print summary of cache database

Hans Vasquez-Gross havasquezgross at ucdavis.edu
Fri Apr 8 11:12:49 BST 2016


I'm using VEP to annotate some VCF files using an offline cache database.
The summary file lets me know the number of overlapped genes/transcripts.
However, it doesn't say how many total genes/transcripts in the database
which would be useful for some calculations.

To annotate, I use the following command to run VEP:
./variant_effect_predictor.pl -species triticum_aestivum -i input.vcf -o
output.vep.vcf --fork 4 --offline --db_version 22

I've been to the cache directory: .~/vep/triticum_aestivum/22, and tried
looking at the storage structure. I saw these are gzipped files within
directories for each contig.

Is there an easy way to get a list of all transcripts/genes in this
database? Thank you.

Cheers
-Hans
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