parameters in bwa mem
0
2
Entering edit mode
5.8 years ago
BioinfoNovice ▴ 110

Hi,

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.

 

Tools bwa bwa mem parameters • 2.4k views
ADD COMMENT

Login before adding your answer.

Traffic: 1585 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6