This is such a basic question coming from lack of experience. I was trying to run freebayes on 2 pools of samples (one with N=37 individuals and other with N=21). I'm using the option --pooled-discrete but I'm not sure on how to set --ploidy and --use-best-n-alleles. Can anyone help me figure out if, for diploid species, ploidy is double the number of samples you pool?
I know it's the number of genome copies per-pool but when I set --ploidy 74 (without --use-best-n-alleles) it keeps eating up all my memory and it never finishes (it's been 3 days). I'm calling only in a small region of a chromosome so it shouldn't take so long, right?
Thanks in advance :)