Hello there, There is a lot of software available for CNV analysis. However, I was wondering if anyone had a particular preference for Ion Torrent based targeted panel data? In particular, I am interested in analyzing the 409 gene panel NGS data from Ion Proton to identify CNVs using the read-depth method. If anyone has any experience and pointers regarding the pros and cons, that would be great! Thank you in advance!
I've used CNVkit on Ion Proton data. It wasn't as clean as Illumina, but the results were definitely usable. Another program OncoCNV is designed to work well on targeted amplicon sequencing data. Is your 409 gene panel using hybrid capture or amplicon sequencing?