Quality scores and sequence alignment

[warrenemmett]

Hi,

I recently had a discussion with someone about the use of quality scores in alignment (specifically related to SNP discovery). As far as I remember there was some debate but at the time most people seemed to think it didn't improve results greatly. I'm interested in what the view is of using quality scores these days and what the results have been if so.

Lastly, are there any other alignment packages you can recommend that can replace MAQ as an aligner that uses quality scores?

Any advice is greatly appreciated!
w