NgsAdmix

This will contain the program called NGSadmix, which is a very nice tool for finding admixture. It is based on genotype likelihoods or genotype probabilities. It is a fancy multithreaded c/c++ program

Installation

wget popgen.dk/software/NGSadmix/ngsadmix32.cpp 
g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix

Input Files

The current input files are the widely used beagle inputfiles, or beagle imputed outputfiles [1]. We recommend ANGSD for easy transformation of Next-generation sequencing data to beagle format.

Options

./NGSadmix
Arguments:
	-likes Beagle likelihood filename
	-K Number of ancestral populations
Optional:
	-fname Ancestral population frequencies
	-qname Admixture proportions
	-outfiles Prefix for output files
	-printInfo print ID and mean maf for the SNPs that were analysed
Setup:
	-seed Seed for initial guess in EM
	-P Number of threads
	-method If 0 no acceleration of EM algorithm
	-misTol Tolerance for considering site as missing
Stop chriteria:
	-tolLike50 Loglikelihood difference in 50 iterations
	-tol Tolerance for convergence
	-dymBound Use dymamic boundaries (1: yes (default) 0: no)
	-maxiter Maximum number of EM iterations
Filtering
	-minMaf Minimum minor allele frequency
	-minLrt Minimum likelihood ratio value for maf>0
	-minInd Minumum number of informative individuals

Output Files

Program outputs 3 files.

1. PREFIX.log
2. PREFIX.fopt.gz
3. PREFIX.qopt

log

• v32 june 25-2013; modified code such that it now compiles on OSX
• v31 june 24-2013; First public version.