I have three pools of hiseq data where N=20,20, & 40 individuals per pool. I sequenced to ~10x depth for each pool. I would like to use the ploidy setting to estimate probable genotypes from each pool, but I'm torn because it doesn't seem correct to estimate 20 or 40 genotypes from pools that have only been sequenced to 10x depth (only 10 chromosomes could have been sampled). So in such a case, would it be more advisable to set the ploidy level to the depth level of 10 and estimate 5 genotypes per pool?
Thank you very much!