How does BWA deal with multi mapping reads?

[metheuse]

Bowtie manual clearly says the default mode is to report one alignment per read, and it will be random choice when tied.

BWA doesn't seem to be quite clear at this point in its manual. Can anyone explain to me how BWA reports alignments if a read can be mapped to multiple locations? If I want it to report only one, which parameter should I use for that?

I'm particularly asking for BWA aln because I'm mapping 50bp SE reads. But it would be even better if you could also explain for BWA mem if it's different.

Thanks a lot!

[GenoMax]

http://seqanswers.com/forums/showthread.php?t=40746

[metheuse]

http://seqanswers.com/forums/showthread.php?t=40746

Thanks, but I read that post before posting my questions.

There are controversial replies in that post. One reply says BWA makes random choice when there is a tie, but the last reply says: "if there are two equal-scoring locations, bwa gives both a mapping score of 3 (equivalent to 50% probability), and so forth."

If the latter reply is true, it's still not clear to me if I can set some parameter to restrict BWA to report only one location (and how). Bowtie chooses one randomly but BWA's manual doesn't say anything about it.

[Brian Bushnell]

For bwa-aln, apparently, the assignment is done after alignment in the sam-file generation phase:

samse bwa samse [-n maxOcc] <in.db.fasta> <in.sai> <in.fq> > <out.sam>

Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.

I'm not sure about bwa-mem.

[metheuse]

For bwa-aln, apparently, the assignment is done after alignment in the sam-file generation phase:



I'm not sure about bwa-mem.

Yes I read that and was wondering what "Repetitive hits will be randomly chosen." exactly means...
If it means choosing a random alignment when multiple locations are found to be equally best, then it's indeed what I need.
I think sampe is equivalent to samse, but the former is for bwa mem.
Thanks!

[Brian Bushnell]

Yes I read that and was wondering what "Repetitive hits will be randomly chosen." exactly means...
If it means choosing a random alignment when multiple locations are found to be equally best, then it's indeed what I need.
I think sampe is equivalent to samse, but the former is for bwa mem.
Thanks!

Sampe and samse have the same description, and yes, the description means reads with multiple equally-scoring alignments.