I am studying Neanderthal ancestry in modern populations from two different regions of the world. These two regions have relatively similar levels of Neanderthal ancestry, and they aren't that far from each other. I have SNP data from an Affymetrix genotyping array (the data are in Plink format) for these populations as well as for the corresponding sites from Neanderthal and Denisovan genomes.
Using the SNP data, I need to try to find out if they have Neanderthal haplotypes in the same parts of their genome. I've found a map of putative Neanderthal introgressed haplotypes from 1000 Genomes Project's European and East Asian genomes (http://akeylab.gs.washington.edu/Vernot_2014/all_haplotypes_populations.bed.files.tgz). I have over 140,000 SNPs that overlap with these haplotypes, and I have two Neanderthal genomes within my Plink dataset.
I want to find a way to determine the Neanderthal allele frequency across these >140,000 sites in both geographical regions (and then graphically depict them).
Any guidance or suggestions?