export VEP_PATH=$HOME/vep
export VEP_DATA=$HOME/.vep
mkdir $VEP_PATH $VEP_DATA; cd $VEP_PATH
curl -LO https://github.com/Ensembl/ensembl-tools/archive/release/86.tar.gz
/usr/local/Cellar/gnu-tar/1.29_1/bin/tar -zxf 86.tar.gz --starting-file variant_effect_predictor --transform='s|.*/|./|g'
rsync -zvh rsync://ftp.ensembl.org/ensembl/pub/release-86/variation/VEP/homo_sapiens_vep_86_GRCh37.tar.gz $VEP_DATA
perl convert_cache.pl --species homo_sapiens --version 86_GRCh37 --dir $VEP_DATA
# Install the Ensembl API, the reference FASTAs for GRCh37/GRCh38/GRCm38, and some neat VEP plugins:
perl INSTALL.pl --AUTO af --SPECIES homo_sapiens --ASSEMBLY GRCh37 --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA
perl convert_cache.pl --species homo_sapiens --version 86_GRCh37 --dir $VEP_DATA
# Download the ExAC r0.3.1 VCF with germline variants called across thousands of normal samples excluding TCGA:
curl -L ftp://ftp.broadinstitute.org:/pub/ExAC_release/release0.3.1/subsets/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz > $VEP_DATA/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz
Last active
November 7, 2016 19:03
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