SNP calling for Cell lines - how does the ploidy affect HC
I am calling SNPs in various immortalised cell lines, which are known to be very instable - hence the ploidy is not known. Generally it should be diploid. So my question is - what can happen if the ploidy is not correct? Would HC miss SNPs? I see a relatively low overlap of common SNPs between two related cell lines and I want to make sure this low overlap is indeed there.
Thank you in advance.