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| 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.
| | NGSadmix is a tool for estimating individual admixture proportions low depth sequencing data based on genotype likelihoods |
| It is a fancy multithreaded c/c++ program
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| =Installation=
| | The software including tutorials can be found here |
| | | https://github.com/aalbrechtsen/NGSadmix |
| <pre>
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| wget popgen.dk/software/NGSadmix/ngsadmix32.cpp
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| g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix
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| </pre>
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| =Input Files=
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| 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.
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| =Options=
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| <pre>
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| ./NGSadmix
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| Arguments:
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| -likes Beagle likelihood filename
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| -K Number of ancestral populations
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| Optional:
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| -fname Ancestral population frequencies
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| -qname Admixture proportions
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| -outfiles Prefix for output files
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| -printInfo print ID and mean maf for the SNPs that were analysed
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| Setup:
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| -seed Seed for initial guess in EM
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| -P Number of threads
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| -method If 0 no acceleration of EM algorithm
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| -misTol Tolerance for considering site as missing
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| Stop chriteria:
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| -tolLike50 Loglikelihood difference in 50 iterations
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| -tol Tolerance for convergence
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| -dymBound Use dymamic boundaries (1: yes (default) 0: no)
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| -maxiter Maximum number of EM iterations
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| Filtering
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| -minMaf Minimum minor allele frequency
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| -minLrt Minimum likelihood ratio value for maf>0
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| -minInd Minumum number of informative individuals
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| </pre>
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| =Output Files=
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| Program outputs 3 files.
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| # PREFIX.log
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| # PREFIX.fopt.gz
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| # PREFIX.qopt
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| =log=
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| * v32 june 25-2013; modified code such that it now compiles on OSX
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| * v31 june 24-2013; First public version.
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