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Code to do data processing and create figures for "The geography of recent genetic ancestry across Europe", http://arxiv.org/abs/1207.3815

branch: master
README
This is the collection of codes used in analysis of european POPRES data
(see Nelson et al, http://www.ncbi.nlm.nih.gov/pubmed/18760391; 
obtain access to data at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000145.v1.p1 .)
for the paper "The geography of recent genetic ancestry across Europe", 
by Peter Ralph and Graham Coop, 
published May 7, 2013, in PLoS Biology, at
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001555

To see what makes what, see the makefile.

Most of the files are pretty clean, but a few have some clutter.

None will actually do anything without obtaining the POPRES data and running BEAGLE http://faculty.washington.edu/browning/beagle/beagle.html on them.

Please use these if they are useful, and credit us if appropriate.

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Notes:

* The .gmap files provide a mapping from the endpoint indices that BEAGLE uses to genetic distances (e.g. in centiMorgans).  Important: BEAGLE uses 0-based indices.

* BEAGLE 4.0 is out, and improved over the version we used (3.3).
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