BioX::Wrapper::Gemini::Examples - Documentation describing the use of the BioX::Wrapper::Gemini module.
For more detailed Gemini usage please refer to the gemini documentation at L:<Gemini Read the Docs|http://gemini.readthedocs.org/en/latest/>.
This set of commands creates an (obviously fake) vcf file, compressed vcf file, and the correct directory structure.
mkdir example cd example touch test1.vcf touch test2.vcf.gz echo "#!/bin/bash" > gemini_process.sh gemini-wrapper.pl --indir `pwd` --outdir `pwd`/processed >> gemini_process.sh
Gemini wrapper creates your directory structure for you. If the --outdir option does not exist it will be created for you.
/example gemini_process.sh /processed /gemini-wrapper /gemini_sqlite /norm_annot_vcf test1.vcf test2.vcf.gz
The normalized compressed vcf files will be in process/gemini-wrapper/norm_annot_vcf .
The sqlite databases will be in /processed/gemini-wrapper/gemini_sqlite .
#!/bin/bash ####################################################################### # This file was generated with the following options # --indir /home/user/example # --outdir /home/user/example/processed ####################################################################### ####################################################################### # Starting Sample Info Section ####################################################################### # test1, test2 ####################################################################### # Ending Sample Info Section ####################################################################### ####################################################################### # Starting Bgzip Section ####################################################################### # The following samples must be bgzipped before processing can begin # /home/user/example/test1.vcf ####################################################################### bgzip /home/user/example/test1.vcf && tabix /home/user/example/test1.vcf.gz wait ####################################################################### # Finished Bgzip Section ####################################################################### ####################################################################### # Normalizing with VT and annotating with SNPEFF the following samples # test1, test2 ####################################################################### bcftools view /home/user/example/test1.vcf.gz | sed 's/ID=AD,Number=./ID=AD,Number=R/' \ | vt decompose -s - \ | vt normalize -r $REFGENOME - \ | java -Xmx4G -jar $SNPEFF/snpEff.jar -c \$SNPEFF/snpEff.config -formatEff -classic GRCh37.75 \ | bgzip -c > \ /home/user/example/processed/gemini-wrapper/norm_annot_vcf/test1.norm.snpeff.gz && tabix /home/user/example/processed/gemini-wrapper/norm_annot_vcf/test1.norm.snpeff.gz bcftools view /home/user/example/test2.vcf.gz | sed 's/ID=AD,Number=./ID=AD,Number=R/' \ | vt decompose -s - \ | vt normalize -r $REFGENOME - \ | java -Xmx4G -jar $SNPEFF/snpEff.jar -c \$SNPEFF/snpEff.config -formatEff -classic GRCh37.75 \ | bgzip -c > \ /home/user/example/processed/gemini-wrapper/norm_annot_vcf/test2.norm.snpeff.gz && tabix /home/user/example/processed/gemini-wrapper/norm_annot_vcf/test2.norm.snpeff.gz wait ####################################################################### # Finished Normalize Annotate Section ####################################################################### ####################################################################### # Gemini is loading the following samples # test1, test2 ####################################################################### gemini load -v /home/user/example/processed/gemini-wrapper/norm_annot_vcf/test1.norm.snpeff.gz \ -t snpEff \ /home/user/example/processed/gemini-wrapper/gemini_sqlite/test1.vcf.db gemini load -v /home/user/example/processed/gemini-wrapper/norm_annot_vcf/test2.norm.snpeff.gz \ -t snpEff \ /home/user/example/processed/gemini-wrapper/gemini_sqlite/test2.vcf.db wait ####################################################################### # Finished Gemini Load Section #######################################################################
BioX::Wrapper::Gemini assumes you have environmental variables set for the SnpEff install ($SNPEFF), reference genome ($REFGENOME).
You can change this with
gemini-wrapper.pl --ref /path/to/reference.fa --snpeff /path/to/snpeff
If you change the snpeff variable you will probably need to change the snpeff_opt
gemini-wrapper.pl --snpef_opt "-c /path/to/snpeff/snpEff.config -formatEff -classic GRCh37.75"
The gemini db_load_opts has the default set as " -t snpeff". If you would instead like to load it with "--skip_cadd --cores 3 -t snpeff" look at the following.
gemini_wrapper.pl --db_load_opts "--skip_cadd --cores 3 -t snpeff"
This can be easily accomplished with environment modules. For more information please refer to the modules documentation. http://modules.sourceforge.net/
For more functional documentation check out the wikipedia page. https://en.wikipedia.org/wiki/Environment_Modules_(software)
For easy install try
sudo yum install environment-modules
See what the variables are with
env |grep MODULE
You can create a custom module path with
export MODULEPATH=/path/to/user/modules:$MODULEPATH
#%Module1.0####################################################################### ## SnpEff modulefile ## proc ModulesHelp { } { puts stderr "\tAdds the snpeff binaries to your path.\n module load snpeff \n java -jar $SNPEFF/snpEff.jar -c /path/to/configuration/file/snpEff.config <args>" } module-whatis "Adds the snpeff binaries to your path." module add java/jdk1.7.0_67 set ROOT_DIR /system/apps/software setenv SNPEFF $ROOT_DIR/snpEff #For analysis and denormalizing module add samtools/1.2 prepend-path PATH $ROOT_DIR/vt
Add in a VEP workflow option
Jillian Rowe <jillian.e.rowe@gmail.com>
This module was originally developed at and for Weill Cornell Medical College in Qatar. With approval from WCMC-Q, this information was generalized and put on github, for which the authors would like to express their gratitude.
To install BioX::Wrapper::Gemini, copy and paste the appropriate command in to your terminal.
cpanm
cpanm BioX::Wrapper::Gemini
CPAN shell
perl -MCPAN -e shell install BioX::Wrapper::Gemini
For more information on module installation, please visit the detailed CPAN module installation guide.