Bwa Alignments With Gaps

Question

[lob]

I am looking for a description of bwa algorithm for mapping with gaps. More precisely I wonder how bwa handles mismatches in reads with gaps. Does it have the same maximum mismatches allowed than when there is no gaps? Does someone know where I can find a cleared description of bwa gapped alignment algorithm?

Thanks

[nilshomer]

There are three alignment algorithms within bwa. Do you mean "bwa aln" (backtrack), "bwa bwasw" (bwa smith-waterman), or "bwa mem" (maximal-exact-matching)? I assume the first since you are talking about "maximum mismatches". I would suggest reading Heng Li's original BWA paper and post specific questions.