The frontline support team will be offline as we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and available to answer questions on the forum on March 25th 2019.
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.