My model system uses a reference genome from a population that is likely highly derived. I have whole genome sequencing data from two other pops, one (we can call PopB) is likely derived from the other (PopA), and both sets of reads were aligned to the reference. In short I want to take a set of polymorphisms that are fixed/nearly fixed in PopA (that are absent in the reference) and flip which allele is considered the reference in both sets of data. Multiple tests I want to do require the identification ancestral state/assumes ref=ancestral which is not the case in about 15% of the variants. I was able to simply make a list of Chromosome/positions that I want to flip the ref/alt definitions but I don't know of a way to use this list to actually flip them. I'd appreciate any help.