PFB file for HumanExome-12v1_A

[pc1]

Hi.

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

I need a population frequency of the b allele/PFB file that corresponds to this chip to get PennCNV to run.

The 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 the PFB file that came with PennCNV to HG19.

I was planning to next match the genotype data 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 lab 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 what I should do, generate a new PFB file using other samples from the same chip type?

I am new to this area. Any help would be much appreciated.