Hi.

I'd like to use PennCNV with Infinium Human Exome BeadChip (HumanExome-12v1_A) genotype data to detect CNVs.

The population frequency of the b allele/PFB file in the PennCNV package required for this is for HG18 and does not contain RSIDs, I think it is Illumina's own IDs (e.g. exm-IND1-200449980). I used liftOver to update to HG19.

I was planning to then match by coordinates as the genotype data does not have RSIDs.

However, it seems like the coordinates don't match up - the updated hhall.hg19.pfb coordinates don't correspond with the Infinium SNP coordinates

I could ask the genotype people to create a new PFB file for me but I don't know if they have enough samples to do that - the PennCNV documentation says that you need 100s to do that. Is that the answer? I am very new to this area.

Any help would be much appreciated.