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How to Run ANNOVAR

Setting ANNOVAR in your environment

To set up your environment to use ANNOVAR, use the module command:

module load annovar

See How to use the module command for further information.

Running ANNOVAR to prepare local annotation databases (requires network connectivity)

Preparation of local annotation databases using ANNOVAR requires network connectivity outside of the Hoffman2 cluster. This step should be performed from the Hoffman2 transfer node (named dtn2). The trasnfer node can be accessed from outside Hoffman2 using the command:

ssh login_id@dtn2.hoffman2.idre.ucla.edu

or, from any node of Hoffman2, with:

ssh dtn2

From the tranfer node (dtn2) load ANNOVAR in your environment:

module load annovar

and use the ANNOVAR command to prepare a local annotation database:

annotate_variation.pl -downdb [optional arguments] <table-name> <output-directory-name>

Running ANNOVAR for tasks that do not require network connectivity

To use ANNOVAR, for any task that does not require network connectivity outside of the Hoffman2 cluster, request an interactive node with qrsh (see: How to Get and Interactive Session through UGE for further information) and invoke ANNOVAR as needed; or, for batch execution, prepare a script to submit to the queues containing the sequence of ANNOVAR commands needed (see: Running a Batch Job for further information).

References

  • http://www.openbioinformatics.org/annovar/
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