I am using bwa mem to do alignments, and I want to get all the alignments in the output. So I use "-a" option of "bwa mem" to do this. But from the output, it seems not all the alignments are reported.
To validate, I run a simple test, I put one query A with length 600bp in a file "read.fq", and then I put three string A1, A2, B in the subject file "ref.fa", where A1 and A2 are exactly same as A, and B (length 2800bp) contained A (not exactly, with some mismatches). Then I run "bwa mem -a ref.fa read.fq" (ref.fa is indexed firstly), but only two alignments(A and A1 as primary, A and A2 as supplementary) are reported.
Any one can help to explain why the alignment with A and B is not reported? Does "bwa mem -a" only reports the higher scored alignments? Or I did some thing wrong? Thank you.