VEP verisoning and GRCh37 vs GRCh38. conda/mamba/anaconda
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2.0 years ago
jon.klonowski ▴ 150

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 • 877 views
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