Detecting SNV in human populations
First thank you a lot for your amazing work on this forum. My project deals with discovering rare population-specific variants in human exomes, and I would like to know how the VQSR step would affect the discovery of these variants. I was wondering whether it is better to perform VQSR on all the populations together (420 individuals but with a risk to clean out "true" rare population-specific variants ) or to run it by population (between 30 and 100 individuals each but I read that VQSR is loosing power with a reduced number of samples) ?
Thank you for your help,