Question: parameters in bwa mem
gravatar for BioinfoNovice
2.1 years ago by
BioinfoNovice90 wrote:


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.


bwa bwa mem tools parameters • 1.0k views
ADD COMMENTlink written 2.1 years ago by BioinfoNovice90
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