I am a graduate student who is still relatively a n00b to bioinformatics and is currently utterly and completely lost.
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 Affymetrix Human Origins array SNP data (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 European and East Asian genomes (http://akeylab.gs.washington.edu/Vernot_2014/all_haplotypes_populations.bed.files.tgz).
I am trying to figure out where the individuals from each population have Neanderthal haplotypes and how they differ between populations.
Does anyone have guidance on how I should proceed?