I have read that for bwa-aln
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.
and for bwa-mem
This post (http://seqanswers.com/forums/showthread.php?t=51081) refers to a post that states that "BWA makes random choice".
Is it possible to set a seed or in some other way ensure that bwa-aln and bwa-mem are deterministic? i.e same reads => same mapping.
I am seeing a case where 2 runs of the same analyses gives different results due to random mapping of some shorter reads (post trimming).
Thanks
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