How do I make bwa-mem and bowtie2 less stringent?
Hi there, I am trying to detect indels in my E. coli samples from an experiment. I am not able to pick up many indels and the ones I do tend to be very small in size. 1-2 bases. Is there a way to make my aligner less stringent (I'm trying both bwa-mem and bowtie2) so that I have more reads mapping to the reference genome? Any help appreciated!
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