This topic has been discussed on many occasions however I couldn't find the right answer afterall.
I am aligning Illumina generated paired-end reads on reference genome with BWA. My understanding is that when BWA finds multiple equally perfect alignments for one read, it will report/map that read randomly. However, I couldn't find an option for discarding these reads, i.e. similar to
-m1 option from bowtie (there is a specific reason why I want to use bwa over bowtie).
Did I miss something or...?