Admixture Analysis

This method performs an admixture analysis using ngsAdmix, please see their tutorial page for full details on this method.

---

Note:

This method requires output from site frequency spectrum to run

Please calculate a site frequency spectrum before performing admixture analysis

---

Basic Usage

To run this method, use the following command

angsd-wrapper Admixture Admixture_Config

where Admixture_Config is the full path to the configuration file for the 2D site frequency spectrum and F_ST estimations.

Input files

All inputs should be specified in Admixture_Config.

Common Variables

This method does make use of Common_Config, those that are used are listed below:

Variable	Function
PROJECT	Name given to all outputs in ANGSD-wrapper
SCRATCH	Place to store files, the full path is SCRATCH/PROJECT/Admixture

Method-Specific Variable

This variable is specific to this method:

Variable	Function
LIKELIHOOD	The likelihood file calculated from the site frequency spectrum, this should be the <PROJECT>_SFSOut.beagle.gz file

Method Parameters

The parameters for this method can be tweaked as necessary, they have been set for optimal generalized function:

Parameter	Function
K	Maximum number of ancestral populations to be inferred
N_CORES	Number of cores to use, please do not set above the limits of your system
MIN_MAF	Minimum minor allele frequency filter

Output files

To be fixed

Naming Scheme	Contents
PROJECT.k.filter	stuff
PROJECT.fopt.gz	Compressed estimate of frequency at each site for population of size k
PROJECT.k.log	Information about running of analysis for k populations
PROJECT.k.qopt	Admixture proportions for all individuals from k populations

Where k is the number of populations being tested.

Visualization

PROJECT.k.qopt files can be visualized with the Shiny graphing interface. A web browser with a graphical user interface is required.