Validates consistency of the aligner interface by taking reads already aligned by BWA in a BAM file, stripping them of their alignment data, realigning them, and making sure one of the best resulting realignments matches the original alignment from the input file.
|--BWTPrefix||String||NA||Index files generated by bwa index -d bwtsw|
Index files generated by bwa index -d bwtsw. The supporting BWT index generated using BWT.
GATK version 2.3-9-ge5ebf34 built at 2013/01/11 22:47:55.