CNV analysis in Hail


#1

I know there was an inquiry about this in 2016, but has there been any change to include CNV analysis, or rather that upon import of CNV VCFs that we are able to perform the necessary analysis without having to perhaps deploy additional tooling like GenomeSTRiP, SOAPsv, SMuFin, MrCaNaVaR, etc? In case of the latter, would perhaps something like ADAM/CANNOLI be recommended to wrap these?

Thanks, Ryan


#2

I think that most discussion around CNV stuff in 2016 had to do with whether we could import + do tertiary analysis on CNV VCFs. In 0.2, we totally can! All schemas have been made totally generic to support use cases like this.

Hail doesn’t do CNV calling though, nor is that on any short- or long-term roadmap. So you’ll still need to use other tools to generate the CNV callset.