Hi, my name is Phillip Richmond and I'm a researcher at the University of Colorado--Boulder. I'm using the SVmerge package which includes the Breakdancer-max program. I am calling structural variants against the mouse genome for an inbred line with different library types, and I was wondering the best way to run your program with these different libraries.
My libraries:
Standard short-insert paired end library from Illumina (2x100, insert~300). (~400m paired reads)
Illumina long-insert mate-pair library from the new protocol with both 4kb and 10kb libraries. (~50m paired reads each for 10k and 4k libraries)

I was wondering if it makes sense to run them all together, or to run them independently and merge the results. From some preliminary testing it seems that having multiple libraries in a single run changes the calls that would be made if they were run independently.

Any help you can have on the subject will be greatly appreciated.


Last edit: Phillip Richmond 2014-04-01