The purpose of this project is to annotate the ancestral alleles of the human-primate ancestor. We used the parsimony-like method used by the 1000 Genomes Project and Ensembl. See section 8.3 of the of the supplementary material from this paper .
Instead of using a multiple-genome alignment produced by the Enredo-Pecan-Ensembl pipeline, we use Progressive Cactus, which also infers the ancestor's genomes.
Running snakemake --cores 22 --configfile configs/8_way_single_copy_hg38.yaml -s calc_ancestor_allele.smk
will create a fasta of each autosome, containing the ancestral allele based in hg38.
See example config file for more details on required files.