I am using pennCNV for copy number to generate genotype clusters, using data from Affy6.0. The function generateaffygeno_cluster.pl takes input affygw6.hg18.pfb (provided by pennCNV package) as reference. However, this pfb file is based on hg18, as indicated by its title.
How would I convert it into a file based on hg19? I found this discussion http://biostar.stackexchange.com/questions/1622/pfb-file-for-cnv-analysis-using-illumina-610-quad-v1-arrays on the forum. However, my problem is different from this one as I am trying to convert between different genome versions. Can anyone give a hint on how to do this? Can I use liftover to do this convertion? And how would that be done? Thank you very much!