9.5 years ago by
Washington University in St. Louis, MO
You need to clarify whether you're looking for Structural Variants (SV) or Copy-number Variants (CNV) or both. Copy-number calls are generally based on read-depth and it shouldn't matter whether your data is paired-end or not. There are several tools that will happily call copy number from single-sample, single end data. (for example readDepth). Tools that you mention like Breakdancer, on the other hand, are looking for structural rearrangement specifically by using discordantly mapping read pairs.
If you're using exome data that's a whole different ballgame, though. You don't have whole-genome coverage and differences in probe affinities make the read depth vary wildly. Thus calling CNVs with single-sample data is challenging at best. To my knowledge, there are no existing tools that do this.
There is one tool I know of that can make fairly good copy-number calls from paired tumor-normal exome sequencing data, and that's VarScan, but you're unlikely to find it useful since you don't have a paired sample.
**disclaimer. I wrote the readDepth package and contributed to the VarScan2 paper (currently in review)