Alignment with BWA: how to discard multi mappers?

Question

[ThePresident]

Hello,

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...?

Thanks

[Asaf]

You can screen the bam file afterwards for reads with no other hits.

Answer 1

[igor]

There is no parameter you can use, but you can filter the BAM with samtools. See this previous discussion: BWA mem how to know if a read is mapped uniquely? and Bwa-Mem: Discriminate Between Reads Mapping Uniquely And Those Mapping In Multiple Positions