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PoisonAlien/dl_vep_cache.sh

Created June 27, 2023 11:47
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dl_vep_cache.sh
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
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