[maq-help] simulate parameters

[Ben B. <be...@gm...>]

Hi Heng or others who might know ..

I am using "maq simulate" to generate some solexa data.  I used the  
default parameters, but i am confused about "-R" - it says "fraction  
of 1bp indels" (default 0.1).  I don't really understand what this  
refers to , 10% seems awfully high.  Does someone have more details.   
Also for the mutation rate "-r" parameter, are these just uniformally  
distributed or based on hapmap or something.

I'm trying to incorporate this into a report today, so if anyone knows  
the answer please let me know.

Thanks!
ben.