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Using Admixture

This is a tutorial on how to use Admixture, which is an ancestry inference tool.

Installations

Note: Jupyter notebook, R, and plink should already be installed in your conda environment at this point. If you do not, visit the pca and plotting tabs

Admixture:

conda install -c bioconda admixture

Using Admixture

Admixture is a fairly easy tool to use. The terminal command is as follows:

admixture <Bed File Path> K
  • K is the number of theoretical source populations
  • The BED file is combined to contain both query and reference datasets

Output

This will create two output files:

  1. <File header>.Q file: Contains the ancestry fractions for each individual
  2. <File header>.P file: Contains the allele frequencies for each individual

The .Q.K file is generally the file of interest when looking to plot ancestry compositions for a given dataset.