Hi. I am looking for reference human genome fasta files (preferably hg38) where the SNP alleles contributing to the reference sequence are always the ancestral alleles, not the "reference" alleles. Any insight into how reference alleles are assigned or became the reference alleles would also be appreciated.
My other option is to edit the SNP loci in the reference genome to the ancestral alleles fetched from the Ensembl variation database, but I thought I would check if the Fasta files I am looking for already exist. I know an hg38 with SNPs coded by the IUPAC ambiguity codes exists. I also came across a "common ancestor" (presumably between Chimps and Humans) build, but this is not exactly what I need.