bwa mem, the -a option

[bsigurjonsson]

Hi all,

From the bwa documentation:
"-a Output all found alignments for single-end or unpaired paired-end reads. These alignments will be flagged as secondary alignments."

Can someone explain to me what this flag does.
I'm working with merged reads, and I'm trying to find gene fusions. Until now I've mainly been using supplementary reads, but I'm exploring other areas of the bwa mapper.

Thanks,
Bjarki