[ensembl-dev] chromosome name from cache file

[Will McLaren]

Hi Afif,

You may provide a tab-delimited chromosome synonyms file to VEP that maps
(in either direction) the names of your chromosomes as input to the names
of the chromosomes as found in the VEP cache. Here we create a simple one
as you only require mapping between one chromosome name set!

$ echo "Chromosome\t1" > chr_synonyms.txt
$ [vep_command] --synonyms chr_synonyms.txt

Hope that helps

Will McLaren
Ensembl Variation


On 3 February 2017 at 22:32, Afif Elghraoui <aelghraoui at sdsu.edu> wrote:

> 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
>
>
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