[ensembl-dev] chromosome name from cache file

[Afif Elghraoui]

Hello,

I'm trying to streamline our VEP workflows and there is this
particularly annoying issue in the available cache files regarding the
chromosome name.

We work with the mycobacterium_tuberculosis_h37rv_ASM19592v2 (previously
GCA_000195955.2) cache file, where the chromosome name is "Chromosome"
rather than "1" as we would have expected. We therefore have steps in
our workflow to replace all the chromosome names with "Chromosome" to
run VEP, then change them back to "1" afterwards.

Is there a chance that this can be corrected? If not, is there any way
we can locally modify the cache files afterwards? I tried symlinking
Chromosome to 1, but VEP does not work properly if I do it. The 
compressed files in the cache folder still appear as binary files after
decompressing.

Thanks and regards

Afif

-- 
Afif Elghraoui
Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence
San Diego State University
Alvarado Medical Center
6367 Alvarado Court, Suite 206
San Diego, CA 92120
p. 858-222-0454
http://tuberculosis.sdsu.edu