[Bio-bwa-help] are there any issues with soft-masking or indels

[Ella B. <eb...@uc...>]

Hi There,

Using version 0.6.2-r126, are there any problems with soft-masking? I think
I read that BWA uses all bases, but I just want to confirm this, since I
don't know how I would be notified if there were issues. Also, is there a
way of specifying the number of indels to allow?

Many thanks for your time.

-- 
Ella Bowles
PhD Candidate
Biological Sciences
University of Calgary

e-mail: eb...@uc..., bo...@gm...
website: http://ellabowlesphd.wordpress.com/