I am looking for some advice on which software would be most suitable for detecting structural variation (particularly deletions and duplications > 100kb) that are fixed or at high frequency between two populations. I have low coverage sequence data (4x per sample) from 40 individuals (20 in population A and 20 in population B). The sequencing is illumina paired end 120bp reads with ~ 200 bp insert sizes. I have come across ReadDepth, MrCanavar and Variation Hunter as all being possibly softwares and I was wondering if anyone had any advice on which of these or other software would be most suitable for this task. Ideally I would like to be able to determine what the freqency is of these variants in the populations, rather than pooling the samples from each population, although that could be done.
Some of the software such as MrCanavar and Variation Hunter require remapping with MrFast and time is a factor for these analyses, however ofcourse if they are the best software I will use them (better done right that quickly and wrong). Any feedback and advice is greatly appreciated. Please feel free to ask for additional information.