NgsAdmix: Difference between revisions
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=Input Files= | =Input Files= | ||
The current input files are the widely used beagle inputfiles, or beagle imputed outputfiles [http://faculty.washington.edu/browning/beagle/beagle.html]. We recommend [[ANGSD]] for easy transformation of Next-generation sequencing data to beagle format. | The current input files are the widely used beagle inputfiles, or beagle imputed outputfiles [http://faculty.washington.edu/browning/beagle/beagle.html]. We recommend [[ANGSD]] for easy transformation of Next-generation sequencing data to beagle format. | ||
=Options= | |||
<pre> | |||
./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 | |||
</pre> | |||
=log= | =log= | ||
* v32 june 25-2013; modified code such that it now compiles on OSX | * v32 june 25-2013; modified code such that it now compiles on OSX | ||
* v31 june 24-2013; First public version. | * v31 june 24-2013; First public version. | ||
Revision as of 10:30, 25 June 2013
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
log
- v32 june 25-2013; modified code such that it now compiles on OSX
- v31 june 24-2013; First public version.