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The Spark shell can be used either in Scala or Python. In this case, as SparkBWA is written in Java, only the Scala shell can be used.
To use SparkBWA from the Spark shell, first you need to cd into the SparkBWA build dir
cd target
After that, you need to start the Spark shell indicating that, additionally, you want to use the SparkBWA jar.
spark-shell --jars SparkBWA-0.2.jar"
Of course, in the previous step, you should also indicate the number of executors, memory per executor, etc ...