Output SAM of Bfast run

[jinghanna]

I am trying to use Bfast to map Solid data to a reference genome. I ran through the work flow as suggested in the manual book. Finally I got output files xxx.sam, but I could not make sense of those files.

How can I make use of SAM files? What I wanted to get out of the mapping results are basically the correspondance between reads and matched reference sequences, for example,

Read1 <----> Ref3, matched from starting pos of xxx
Read2 <----> Ref8, matched from starting pos of xxx

Are there some tools available for doing this?

Thanks a lot!

[Simon Anders]

I give you the benefit of doubt that before posting this question, you did the obvious step of searching Google for "SAM file format" and found the SAM specification and read it.

However, given that, I fail to understand your question. The SAM file gives you precisely the correspondence you want; that's the whole point of an aligner output format.

Simon