VEP verisoning and GRCh37 vs GRCh38. conda/mamba/anaconda
0
0
Entering edit mode
2.6 years ago
jon.klonowski ▴ 210

I am trying to use command line VEP. Given that I am using a shared server, I am using conda/mamba to get VEP and set up my environment:

mamba create -n ensembl-vep -c conda-forge -c bioconda ensembl-vep=106

alternatively (but this only gives you v88):

conda create -n ensembl-vep
conda activate ensembl-vep
conda install -c bioconda perl-bioperl-core
conda install -c bioconda perl-bioperl
conda install -c bioconda ensembl-vep
conda deactivate
conda activate ensembl-vep

and next, I have to get the cache files to obtain the FASTA to run VEP. Which leads me to my question: How do we check if GRCh37 (is available/was updated) on different versions of VEP?

I found a post in 2019, where it was said that VEP v95 was the last version with GRCh37 updated/available, how can we check if there were further developments in more recent versions?

It is odd because here: http://useast.ensembl.org/info/docs/tools/vep/script/vep_cache.html It says that GRCh37.p13 is available with vep v.106

however when i run

vep_install -a cf -s homo_sapiens -y GRCh37.p13 -c ./vep_cache/ --CONVERT

or

vep_install -a cf -s homo_sapiens -y GRCh37 -c ./vep_cache/ --CONVERT

I get the error:

ERROR: No matching species found at /data/home/jonathan/conda/envs/ensembl-vep/bin/vep_install line 1168.

However, If I install VEP v95, this command works.

ensembl genomics VEP GRCh37 conda • 1.0k views
ADD COMMENT

Login before adding your answer.

Traffic: 1838 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6