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Warning

Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.

Annovar

ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).

Interactive Usage

After connecting to Iceberg (see Establishing a SSH connection), start an interactive session with the qsh or qrsh command.

To add the annovar binaries to the system PATH, execute the following command

module load apps/binapps/annovar/2015DEC14

Documentation

The annovar manual is available online at http://annovar.openbioinformatics.org/en/latest/

Installation notes

The install is a collection of executable Perl scripts. Installation involves copying the directory and adding it to the PATH. It seems that annovar uses dates to distinguish between releases rather than version numbers

tar -xvzf ./annovar.latest.tar.gz
mkdir -p mkdir -p /usr/local/packages6/apps/binapps/annovar
mv annovar /usr/local/packages6/apps/binapps/annovar/2015DEC14

Modulefile

  • The module file is on the system at /usr/local/modulefiles/apps/binapps/annovar/2015DEC14

Its contents are

#%Module1.0#####################################################################
##
## annovar modulefile
##

## Module file logging
source /usr/local/etc/module_logging.tcl
##

proc ModulesHelp { } {
        puts stderr "Makes annovar 2015DEC14 available"
}

set ANNOVAR_DIR /usr/local/packages6/apps/binapps/annovar/2015Dec14

module-whatis   "Makes annovar 2015DEC14 available"

prepend-path PATH $ANNOVAR_DIR