Question: Best Programs For Local Ancestry
3
gravatar for Zach Stednick
8.4 years ago by
Zach Stednick650
Seattle, WA
Zach Stednick650 wrote:

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?

software R • 2.3k views
ADD COMMENTlink modified 7.7 years ago by Jorge Amigo11k • written 8.4 years ago by Zach Stednick650
3
gravatar for Jorge Amigo
8.4 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

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

main blog: Eurogenes 500K SNP BioGeographicAncestry Project

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).

ADD COMMENTlink written 8.4 years ago by Jorge Amigo11k
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