|
|
| (105 intermediate revisions by 4 users not shown) |
| Line 1: |
Line 1: |
| 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
| |
|
| |
|
| =Installation=
| | The software including tutorials can be found here |
| | | https://github.com/aalbrechtsen/NGSadmix |
| <pre>
| |
| wget popgen.dk/software/NGSadmix/ngsadmix32.cpp
| |
| g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix
| |
| </pre>
| |
| | |
| =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.
| |
| | |
| =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>
| |
| =Output Files=
| |
| Program outputs 3 files.
| |
| | |
| # PREFIX.log
| |
| # PREFIX.fopt.gz
| |
| # PREFIX.qopt
| |
| | |
| ==Log file==
| |
| <div class="toccolours mw-collapsible mw-collapsed">
| |
| Contents of the file log file
| |
| <pre class="mw-collapsible-content">
| |
| <pre>
| |
| -> Dumping file: tskSim/tsk6GL.beagle.s1.log
| |
| -> Dumping file: tskSim/tsk6GL.beagle.s1.filter
| |
| Input: lname=tskSim/tsk6GL.beagle nPop=3, fname=(null) qname=(null) outfiles=tskSim/tsk6GL.beagle.s1
| |
| Setup: seed=1 nThreads=10 method=1
| |
| Convergence: maxIter=2000 tol=0.000000 tolLike50=0.010000 dymBound=0
| |
| Filters: misTol=0.050000 minMaf=0.000000 minLrt=0.000000 minInd=0
| |
| Input file has dim: nsites=100000 nind=75
| |
| Input file has dim (AFTER filtering): nsites=100000 nind=75
| |
| iter[start] like is=9299805.984931
| |
| iter[50] like is=-6531138.892608 thres=0.002800
| |
| iter[100] like is=-6528710.773349 thres=0.001289
| |
| iter[150] like is=-6528405.896951 thres=0.001211
| |
| iter[200] like is=-6528306.803820 thres=0.000420
| |
| iter[250] like is=-6528277.160993 thres=0.000546
| |
| iter[300] like is=-6528271.925055 thres=0.000033
| |
| iter[350] like is=-6528271.177692 thres=0.000008
| |
| iter[400] like is=-6528270.876315 thres=0.000005
| |
| iter[450] like is=-6528270.772894 thres=0.000140
| |
| iter[500] like is=-6528270.747721 thres=0.000002
| |
| iter[550] like is=-6528270.740654 thres=0.000002
| |
| Convergence achived because log likelihooditer difference for 50 iteraction is less than 0.010000
| |
| best like=-6528270.740654 after 550 iterations
| |
| -> Dumping file: tskSim/tsk6GL.beagle.s1.qopt
| |
| -> Dumping file: tskSim/tsk6GL.beagle.s1.fopt.gz
| |
| [ALL done] cpu-time used = 671.82 sec
| |
| [ALL done] walltime used = 114.00 sec
| |
| </pre>
| |
| </div>
| |
| | |
| =log=
| |
| * v32 june 25-2013; modified code such that it now compiles on OSX
| |
| * v31 june 24-2013; First public version.
| |