Looking for a pipeline - SV detection mit mate pair

[tristanstoeber]

Hey guys,

I am trying to set up asimulation to estimate what mate pair coverage I need to detect a big deletion in my cthromosom. The steps I want to perform are listed here:
- randomly insert a big deletion (2000bp) into a copy of my original chromosom
- simulate a Illumina mate pair sequencing with a certain coverage
- map the reads on to the original chromosom
- try to detect structural variations
- repeat this simulation with a different coverage to see what coverage is sufficient

How would you proceed? What software would you use to realistically simulate an Illumina mate pair read regarding contamination, error rate and stuff like Biotin dropdown? What software is suitable for the analysis and the mapping?

Of course I already tried out a lot of approaches myself beforehand, but I would prefer to get a 'de novo'-suggestion without influencing you with the stuff that I tried.

Besides that. Is there a way to statistically calculate the probability of a positive detection? It would be very neat to have a theoretical calculation and to compare the 'real' simulation with it.

Thanks a lot!
Tristan