I am trying to determine local ancestry on an admixed population using YRI and CEU populations from Hapmap as a reference. So far I have tried Hapmix and SABER. Does anyone have any experience using either of these programs or other local ancestry programs?
this is more a suggestion rather than an answer. there is a group of people working on a similar issue, and although they tend to prefer using the RHHcounter/RHHmapper combo.
suggested reading: Locating and visualizing minority non-European admixtures across our genomes
further reading: Taking a closer look at your "Chromosome Mosaic" results
forum entry: http://forumbiodiversity.com/showthread.php?t=8020
I found this project because I found out that they were using our population genetics browser SPSmart to visualize graphically their findings, querying the CEPH data (although you may query the latest HapMap release if desired).