Question about stampy, novoalign, and bwa

[oiiio]

From using both stampy and novoalign, I have noticed that stampy takes a considerably LONGER time than novoalign when mapping to SAMs. I am providing the command line arguments that I used for stampy, and maybe someone here can tell me if I am using the wrong parameters, syntax, etc.

First I recalibrate the bases like this:

stampy.py -g PREFIX -h PREFIX -R file1.fastq file2.fastq

Then I map it like this:

stampy.py -g PREFIX -h PREFIX -o A.sam -M file1.fastq file2.fastq

I am using stampy version 1.0.12 and novoalign version 2.07. Also, is stampy faster when using BWA to pre-map, and would this have an effect on the accuracy?
Thanks,
Gareth

[nilshomer]

Pre-mapping with BWA is faster will little effect on accuracy, though this is better presented in the Stampy paper (check it out!).