CNVkit and Ion Torrent Data - Targeted Sequencing

Question

[quantrum75]

Hello there, I came across this very useful and interesting tool. I have a dataset corresponding to a paired tumor-normal data set for NGS data obtained using the 409 gene panel of Ion Proton. My questions are

1) Does this tool work with Ion Torrent data?

2) Are there any particular caveats to trying this out with Ion data as opposed to the extensive testing on Illumina data that has already been done (The bane of my existence!)

Thanks for the same!

Answer 1

[Eric T.]

Yes, I've used it successfully on Ion Torrent and a few other users have reported that they've done the same. I'd recommend using the most recent CNVkit; also see this recent bug report and provided workaround.