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vep-software
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vep-software [2017/02/06 21:34] joguya created |
vep-software [2019/08/11 18:41] (current) aorth |
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| - | ====== Variant Effect Predictor(VEP) ====== | + | ====== Variant Effect Predictor (VEP) ====== |
| VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, | VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, | ||
| Line 5: | Line 5: | ||
| ===== Information ===== | ===== Information ===== | ||
| - | * Latest Version: | + | * Latest Version: |
| * Added: February, 2017 | * Added: February, 2017 | ||
| - | * Link: http://www.ensembl.org/info/docs/tools/vep/index.html | + | |
| + | | ||
| + | * Annotations: | ||
| ===== Usage ===== | ===== Usage ===== | ||
| Line 14: | Line 16: | ||
| < | < | ||
| - | ===== Installation ====== | + | Load one version into your environment and run it: |
| - | Notes from the sysadmin during installation: | + | < |
| + | $ vep --cache / | ||
| + | </ | ||
| - | < | + | **N.B.** The VEP cache is installed in '' |
| - | - install vep-script | + | |
| - | $ sudo mkdir -p / | + | |
| - | $ sudo chown -R joguya: | + | |
| - | $ cd scripts/ | + | |
| - | $ module load perl/5.22.3 | + | |
| - | $ scl enable devtoolset-3 bash | + | |
| - | $ cpanm File:: | + | |
| - | $ module load htslib/1.3.2 | + | |
| - | $ mkdir / | + | |
| - | $ perl INSTALL.pl --DESTDIR / | + | |
| - | $ PERL5LIB=$PERL5LIB:/ | + | |
| - | $ cp *.pl *.vcf / | + | |
| - | $ sudo chown -R root:root / | + | |
| - | - download cattle annotation data to / | + | ===== Installation ====== |
| - | $ sudo mkdir / | + | Notes from the sysadmin during installation: |
| - | $ sudo chown joguya: | + | |
| - | $ PERL5LIB=$PERL5LIB:/ | + | |
| - | $ sudo chown -R root:root / | + | |
| - | </ | + | |
| + | < | ||
| + | $ curl -L -O https:// | ||
| + | $ unzip 92.1.zip | ||
| + | $ sudo yum install perl-DBI perl-DBD-mysql perl-JSON perl-perlIO-gzip | ||
| + | $ module load htslib/1.6 | ||
| + | $ cd ensembl-vep-release-92.1 | ||
| + | $ cpanm -l . Set:: | ||
| + | $ mkdir cache | ||
| + | $ PERL5LIB=lib/ | ||
| + | $ sudo mkdir -p / | ||
| + | $ sudo cp -r * / | ||
vep-software.1486416888.txt.gz · Last modified: 2017/02/06 21:34 by joguya
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