I would like to know other people opinion about this, because I am mainly used to do RNA-Seq analysis, and I would appreciate some help :)
I have sequenced a human genome with mate paired end reads, and these reads are supposedly big enough to being able to find big indels easily -concretely, I am looking for some big insertions and/or recombinations between different chromosomes-. I am wondering which would be the best pipeline for this, and how to find these structural variants. There are many tools and options, and I am not sure which would be the best or the most usual way to proceed.
Thank you all for your help and patience. I would love to hear your opinion!