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PoisonAlien/dl_vep_cache.sh

Created June 27, 2023 11:47
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  1. PoisonAlien created this gist Jun 27, 2023.
    12 changes: 12 additions & 0 deletions dl_vep_cache.sh
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    Original file line number Diff line number Diff line change
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    pipeline_dir = "./"

    echo "Downloading VEP cache.." 1>&2
    mkdir -p ${pipeline_dir}/resources/vep_cache/
    cd ${pipeline_dir}/resources/vep_cache/
    curl -O https://ftp.ensembl.org/pub/release-107/variation/indexed_vep_cache/homo_sapiens_vep_107_GRCh38.tar.gz
    tar -xzf homo_sapiens_vep_107_GRCh38.tar.gz -C ./

    wget https://ftp.ensembl.org/pub/release-107/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
    gunzip -c Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz | bgzip > Homo_sapiens.GRCh38.dna.primary_assembly.fa.bgzip
    mv Homo_sapiens.GRCh38.dna.primary_assembly.fa.bgzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
    samtools faidx Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz