I have 79 individuals (water buffalo) for which I need to generate a look up table. I have two questions after I came across this post- https://sourceforge.net/p/ldhat/mailman/message/31772311/
1) Since I have 79 individuals, I was using 'complete' program to generate a look up table for each chromosome. (Buffalo has 24 autosomal chromosomes). So, I have .sites and .loc file for each chromosomes. So, should my -n be 158 (=2*79) for every 'complete' run for each chromosome?
2) Is it advisable to use (n=120, theta=0.001 per site) or (n=192, theta=0.001 per site) to generate my own look up table for each chromosome if my look up table generation is going to take a long time? (and use lkgen instead)?