Genomic Resources for Global and Local Ancestry Estimation in a Captive Baboon Colony

VCF files mapped to Panubis1.0 with 881 olive (Papio anubis) and yellow (Papio cynocephalus) baboons from the Southwest National Primate Research Center. VCF files were generated in two separate pipelines, first using Beagle 4.1 and Beagle 5.4 and additionally SHAPEIT5/IMPUTE5 to test if a pedigree-aware software reduced the number of evident phase switch errors. VCFs here have been phased and imputed in their respective pipelines, filtered for imputation accuracy with markers with less than 0.7 confidence removed using BCFTools, and then phase switch corrected using Tractor. Genomic resources (AIMs and Fixed markers) are based off of Panubis1.0 coordinates. Local ancestry estimation completed by RFMix and then phase-switch-corrected using Tractor.