[ensembl-dev] chromosome name from cache file

[Afif Elghraoui]

Hi, Will,

Yes, thank you--that works perfectly. I just had to upgrade to v87 (was
on v84, where this option apparently didn't exist).

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

On 02/06/2017 03:26 AM, Will McLaren wrote:
> 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
>
>

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