Knowing how important this specific area of research is, we are actively developing a pipeline specially tailored for cancer studies. The pre-processing of the data is very much similar to the steps mentioned in the Exon Capture/Whole Genome analysis section.
Since data analysis for cancer is very project specific, the software and methodology for the analysis may vary. We have experience with the tools mentioned in the workflow diagram below to detect low frequency point mutations, indels, large deletions and insertions, copy number variations, inversions, etc. Ultimately, the tool for analysis is dependent on the question that needs to be answered.