Selection against admixture and gene regulatory divergence in a long-term primate field study

Selection against admixture and gene regulatory divergence in a long-term primate field study
Vilgalys & Fogel et al. (bioRxiv)

• Panubis1.0_to_hg38.chain.gz; hg38_to_Panubis1.0.chain.gz: Liftover chain files between Panubis1.0 and hg38. 
• amboseli_LCLAE_tracts.txt.gz: Local ancestry calls for 442 wild, hybrid baboons studied as part of the Amboseli Baboon Research Project. Local ancestry was called using LCLAE and is represented by a 0 for homozygous yellow ancestry, 2 for homozygous anubis ancestry, and 1 for heterozygous ancestry. Each row in the file has a genomic position (chromosome, start, and end), local ancestry call, and the individual for whom the call was made.  
• masked_yellow_and_anubis.vcf.gz: Genotype calls for non-Amboseli yellow and anubis baboons, after masking to remove putative introgressed ancestry. 
• A time-stamped version of the code is included here, and also available on GitHub at github.com/TaurVil/VilgalysFogel_Amboseli_admixture.