CNV detection analysis using R or Matlab

Question

[Beñat]

I am trying to do a CNV detection analysis. I have 3 BAM files from the whole exome, and I know that in one of them there is an amplification in the chromosome 2. I wolud like to know whis is the best method for the analysis. I am able to work with R and MatLab. Thanks!

Answer 1

[Irsan]

Use the off-target data to do copy number analysis, for example with CopyWriteR. Alo see this post: Revolution (?) in CNA detection using exome/targeted sequencing

[Beñat]

Thank you very much for your help Irsan