Just to get you on track :

1 - you have first to index the genome reference (human or other...) : bwa index

2 - then only you will be able to map back your reads to the genome. : bwa aln

3 - Finally depending on your experiment type (single end or paired end) : bwa samse or bwa sampe

For detailed algorithm explanation and parameters specifications, have a look to the link given by Istvan.

Cheers, Tony

Please read the manual first. You will see that it contains the answer to just about all of your present and future questions.

http://bio-bwa.sourceforge.net/bwa.shtml