does bwa mem use base qualities?

Question

[Richard]

Hi all,

I've been looking around on the internet for confirmation that BWA mem doesn't use base qualities. Can anyone confirm that BWA mem does not use the base qualities:

1. To decide where an alignment should be placed
2. To assign a mapping quality

I see in the docs that it does/can use the base qualities if we want to trim off the ends of the reads when the base quality gets low, but this doesn't seem to be recommended for mem.

I see here that BWA mem doesn't use the base qualities for "gapped alignment", but does this also apply to non-gapped alignments?

https://github.com/lh3/mem-paper/blob/master/response_to_aaron.md

I also see here that earlier versions of BWA were confirmed to not use the base qualities for alignment purposes:

http://sourceforge.net/p/bio-bwa/mailman/message/25840739/

I have in the back of my mind that BWA just doesn't use the base qualities, but I'm hoping to put this whole thing to rest.

Thanks,
Richard

Answer 1

[rp7]

Seems like the answer is no, bwa does not use base quality scores:

https://sourceforge.net/p/bio-bwa/mailman/message/34410817/