I am analysing whole genome data, which I splitted into 31 chromosomes. My chromosomes in *.vcf.gz format, span from 100Mb to 7.7Gb. Thus, running a Bayescan analysis per chromosome takes an enormous computation time, specially for the largest chromosomes.
Does splitting the chromosomes in smaller pieces alter the final output of bayescan? Do bayescan calculations involve some statistics that need to take all variants into acount? or is each position calculated independently?