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na399 / popgen-project

Structure and admixture in the Grant's gazelle species complex
https://na399.github.io/popgen-project/
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run TreeMix #3

Open na399 opened 7 years ago

na399 commented 7 years ago

Use plink2treemix.py to convert the file format, the rest should hopefully be straightforward. 

Added a small script to convert stratified allele frequencies output from plink into TreeMix format. 
This will be incorporated into the next release, but for the moment must be downloaded 
separately. To run this, let's say you have data in plink format (e.g., data.bed, data.bim, 
data.fam) and a plink cluster file matching each individual to a population (data.clust).

Now you run:
plink --bfile data --freq --missing --within data.clust
gzip plink.frq
plink2treemix.py plink.frq.gz treemix.frq.gz
na399 commented 7 years ago

use PLINK files from here https://github.com/na399/popgen-project/tree/master/grants_package/processed