ANNOVAR v2016Feb01

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).

Accessing the software

To load the module:

$ module load apps/annovar/v2016Feb01

An example command to include in your job script:

table_annovar.pl $ANNOVAR_EXAMPLE/ex1.avinput \
        $ANNOVAR_HUMANDB -buildver hg19 -out myanno \
        -remove -protocol refGene -operation g -nastring . -csvout

There are two extra, useful environment variables set:

  • ANNOVAR_EXAMPLE refers to the directory with the example that is supplied with ANNOVAR.
  • ANNOVAR_HUMANDB refers to the humandb directory that is supplied with ANNOVAR.

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations

None.

Other Information

The Support Level for this application is An.

Visit the ANNOVAR website for more information regarding this application.


Last modified: 29 September 2017