Changes

</code>

</code>

Replace vc.conf with the approprate path/name of the user's configuration file.

* Replace <code>vc.conf</code> with the path/name of the user's configuration file

 

** If you are not overriding any defaults, you can alternatively specify <code>--list path/bam.list</code> replacing <code>path/bam.list</code> with the path/name of your BAM list file.

If <code>OUT_DIR</code> is not defined in the configuration file, add <code>--outdir</code> followed by the path to the user's desired output directory.

 

* If <code>OUT_DIR</code> is not defined in the configuration file, add <code>--outdir</code> followed by the path to the user's desired output directory.

Update the value following <code>--numjobs</code> to the appropriate number of jobs to be run in parallel.