We would like to use PennCNV and QuantiSNP to call CNVs for new Illumina Omni2.5 array data. These are our normal go-to algorithms for CNV calling. We would like to A) find a way to continue using them or B) find the next best CNV calling algorithm for these arrays.
Problem is PennCNV requires a PFB and HMM file to do CNV calling for these. A PFB file can be generated as Neil showed here. I wondered about the HMM file for the Illumina Omni2.5. I cannot find this anywhere. And I don't know if there is a way to generate it.
I wonder if anyone has solutions that permit either PennCNV or QuantiSNP to be used with the larger Omni2.5 data or, if not, what is the best alternative?