Changes

====Required on Command-Line or in Config File====

====Required on Command-Line or in Config File====

The following Command-Line or Config File Settings must be specified by the user:

The following Command-Line or Config File Settings must be specified by the user:

* --outdir/OUTDIR= path to desired output directory

* --outdir/OUT_DIR= path to desired output directory

====Targeted/Exome Sequencing Settings====

====Targeted/Exome Sequencing Settings====

** WRITE_TARGET_LOCI = TRUE

** WRITE_TARGET_LOCI = TRUE

* Specify the output sub-directory to store target information, for example: targetDir

* Specify the output sub-directory to store target information, for example: targetDir

** Should not be a full path as this will co under the OUTDIR directory.

** Should not be a full path as this will co under the OUT_DIR directory.

** TARGET_DIR = targetDir

** TARGET_DIR = targetDir

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

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

If <code>OUTDIR</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.

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