BWA-MEM Syntax Understanding

Question

[ggman]

Hey all,

I am trying to switch over from bowtie to BWA. There are many options that I don't understand once you attempt to align reads to the reference genome. Would it be better to leave these options as default, especially when it comes to the scoring?

GG

Answer 1

[Devon Ryan]

It's always best to use the defaults when you're first using a new program unless you're already familiar with their implications. That's true for every program you will ever use.

[ggman]

Gotcha, thanks Devon!

[ATpoint]

On top of that, you'll probably have a hard time even finding publications that use it with something other than the defaults, unless the task is something like matching synthetic reporter libraries with intentional small mutations in massively parallel reporter assays.