Running VEP without --cache
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Entering edit mode
21 months ago

I successfully installed VEP but one step that I skipped was the download of the cache file that I need because I can't afford it to be placed in $HOME/.vep due to limited space of $HOME. However, I believe there is no need for cache file and I should be able to run it this way:

/vep/ensembl-tools-release-95/vep --format vcf --json --everything --allele_number --no_stats --offline --minimal --assembly GRCh38 --fasta /vep/homo_sapiens/95_GRCh38/hg38.fa --plugin LoF,loftee_path:/vep/loftee_grch38,gerp_bigwig:/vep/loftee_data_grch38/gerp_conservation_scores.homo_sapiens.GRCh38.bw,human_ancestor_fa:/vep/loftee_data_grch38/human_ancestor.fa.gz,filter_position:0.05,min_intron_size:15,conservation_file:vep/loftee_data_grch38/loftee.sql,run_splice_predictions:0 --dir_plugins /vep/loftee_grch38 -o STDOUT

However, I am getting an error:

MSG: ERROR: Cache directory /opt/seqr/.vep/homo_sapiens not found

How should I modify the current VEP command to still run it? I think previous versions of VEP were just running like that, but the latest 99 is not (or I am just mistaken somehwere).

vep • 2.1k views
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remove --offline and add --database

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Entering edit mode
21 months ago
ATpoint 55k

Please read the manual: https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html

It is possible to run VEP connecting to the public Ensembl database servers in place of a cache. This can be adequate when annotating small files, but the database servers can become busy and slow. To enable this option, use --database

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Ok, then I don't get why both fasta and cache are needed. For the previous version only fasta was there...

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