differential mutation rates across whole genome?

[GoogleCodeExporter]

Hello,

I am interested in using macs to simulate a handful of whole genomes. Yet, I do 
not see a way to assign different mutation rates to different regions in the 
genome. A brute-force way to do so, I guess, is to simulate each region 
separately, but it will require tons of commands to achieve such goal. Would it 
be possible to assign a file, which specifies the mutation rate (a.k.a a value 
for theta) of each region of interest, similar to the recombination map file 
that macs takes?

Thanks,
PingHsun(Benson)

Original issue reported on code.google.com by hsie...@email.arizona.edu on 2 May 2013 at 8:47

[GoogleCodeExporter]

Hi PingHsun,

Unfortunately we don't support such an option in macs currently.  I think what 
you suggested above would not be hard if you looped the runs in a shell script 
however, each run with a different value of theta.

Gary

Original comment by gche...@gmail.com on 2 May 2013 at 8:54

• Changed state: WontFix