I'm using bwa mem to align my 150-bp Illimina reads to a reference genome. I'm trying to understand the parameters as much as I can since I don't want to just execute evertyhing blindfully with defaults.
What is a "band width for banded alignment" (-w) ? How the change for this parameter will affect the alignment overall? And what is "off-diagonal X-dropoff" (-d)?
Your contributions will be very helpful. Thank you very much in advance.