I am running bwa index and it generates several output files out of which few are binary files. The other files such as ".ann and .amb" give me output which I am not able to analyse. Is there a manual which explains the output results ? I tried looking into bwa_indexing manual but I could not find it.
As Devon said, there is no need to spend your time on these files. They are used by BWA internally during the alignment. These files are the burrows-wheeler-transformed genome, the suffix array index, the packed sequence etc, but unless you are interested in alignment theory, ignore them and simply do your alignment.