The gemini db_load_opts hasthe defaultset as " -t snpeff". If you would instead like to load it with"--skip_cadd --cores 3 -t snpeff"look at the following.
This can be easily accomplished withenvironment modules. For more information please refer to the modules documentation. http://modules.sourceforge.net/
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
=head2 Upcoming Functionality
Add in a VEP workflow option
=head1 AUTHOR
Jillian Rowe E<lt>jillian.e.rowe@gmail.comE<gt>
=head1 ACKNOWLEDGEMENTS
This module was originally developed at and forWeill Cornell Medical College in Qatar. With approval from WCMC-Q, this information was generalized and put on github, forwhich the authors would like to express their gratitude.
Keyboard Shortcuts
Global
s
Focus search bar
?
Bring up this help dialog
GitHub
gp
Go to pull requests
gi
go to github issues (only if github is preferred repository)