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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.
| | 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.
| |
|
| |
|
| | | The software including tutorials can be found here |
| Latest version is 32 from June 25 2013. It can be found [http://popgen.dk/software/NGSadmix/ngsadmix32.cpp ]. Older versions can be found here:
| | https://github.com/aalbrechtsen/NGSadmix |
| [http://popgen.dk/software/NGSadmix/].
| |
| | |
| =Installation=
| |
| | |
| <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>
| |
| | |
| =Run example=
| |
| Assuming we have an input file called input.gz and we assume 3 ancestral populations (-K 3), and that we want to use 4 computing cores (-P 4). The prefix of the output files is myoutfiles (-o myoutfiles) using only SNP with af MAF above 5% (-minMaf 0.05).
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| <pre>
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| ./NGSadmix -likes input.gz -K 3 -P 4 -o myoutfiles -minMaf 0.05
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| </pre>
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| | |
| Get example data from the 1000 genomes project (100 individuals from 5 populations with 50000 SNPs)
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| <pre>
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| wget popgen.dk/software/NGSadmix/data/input.gz
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| wget popgen.dk/software/NGSadmix/data/pop.info
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| </pre>
| |
| | |
| =Input Files=
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| Input files are contains genotype likelihoods in genotype likelihood beagle input file format [http://faculty.washington.edu/browning/beagle/beagle.html]. We recommend [[ANGSD]] for easy transformation of Next-generation sequencing data to beagle format.
| |
| | |
| Example of a beagle genotype likelihood input file for 3 individuals.
| |
| <pre>
| |
| marker allele1 allele2 Ind0 Ind0 Ind0 Ind1 Ind1 Ind1 Ind2 Ind2 Ind2
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| 1_14000023 1 0 0.941 0.058 0.000 0.799 0.199 0.001 0.666 0.333 0.001
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| 1_14000072 2 3 0.709 0.177 0.112 0.941 0.058 0.000 0.665 0.332 0.001
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| 1_14000113 0 2 0.855 0.106 0.037 0.333 0.333 0.333 0.799 0.199 0.000
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| 1_14000202 2 0 0.835 0.104 0.060 0.799 0.199 0.000 0.333 0.333 0.333
| |
| ...
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| </pre>
| |
| Column 1:The marker name (the information is not atually used)
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| | |
| Column 2 and 3: the major and minor allele (these two columns are not used within the program).
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| | |
| The rest of the colums are the genotypes likelihoods (not in log space). For each individual we have 3 columns.
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| Note that the above values sum to one per sites for each individuals. This is just a normalization of the genotype likelihoods in order to avoid underflow problems in the beagle software it does not mean that they are genotype probabilities.
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| | |
| The file is allowed to be compressed with gzip.
| |
| | |
| =Options=
| |
| <pre>
| |
| ./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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| -o 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>
| |
| | |
| =Output Files=
| |
| Program outputs 3 files.
| |
| | |
| # PREFIX.log
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| # PREFIX.fopt.gz
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| # PREFIX.qopt
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| | |
| * The log file contains log information of the run. Commandline used for running the program, what the likelihood is every 50 iterations, and finally how long it took to do the run.
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| | |
| * The fopt.gz file is an compressed file, which contains an estimate of the frequency for each site for all populations.
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| | |
| * The qopt file contains the admixture proportions for all individuals.
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| | |
| Examples of the output files are found below.
| |
| | |
| | |
| ==Log file==
| |
| <div class="toccolours mw-collapsible mw-collapsed">
| |
| Contents of the file log file
| |
| <pre class="mw-collapsible-content">
| |
| -> Dumping file: tskSim/tsk6GL.beagle.s1.log
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| -> Dumping file: tskSim/tsk6GL.beagle.s1.filter
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| Input: lname=tskSim/tsk6GL.beagle nPop=3, fname=(null) qname=(null) outfiles=tskSim/tsk6GL.beagle.s1
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| Setup: seed=1 nThreads=10 method=1
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| Convergence: maxIter=2000 tol=0.000000 tolLike50=0.010000 dymBound=0
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| Filters: misTol=0.050000 minMaf=0.000000 minLrt=0.000000 minInd=0
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| Input file has dim: nsites=100000 nind=75
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| Input file has dim (AFTER filtering): nsites=100000 nind=75
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| iter[start] like is=9299805.984931
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| iter[50] like is=-6531138.892608 thres=0.002800
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| iter[100] like is=-6528710.773349 thres=0.001289
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| iter[150] like is=-6528405.896951 thres=0.001211
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| iter[200] like is=-6528306.803820 thres=0.000420
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| iter[250] like is=-6528277.160993 thres=0.000546
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| iter[300] like is=-6528271.925055 thres=0.000033
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| iter[350] like is=-6528271.177692 thres=0.000008
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| iter[400] like is=-6528270.876315 thres=0.000005
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| iter[450] like is=-6528270.772894 thres=0.000140
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| iter[500] like is=-6528270.747721 thres=0.000002
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| iter[550] like is=-6528270.740654 thres=0.000002
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| Convergence achived because log likelihooditer difference for 50 iteraction is less than 0.010000
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| best like=-6528270.740654 after 550 iterations
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| -> Dumping file: tskSim/tsk6GL.beagle.s1.qopt
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| -> Dumping file: tskSim/tsk6GL.beagle.s1.fopt.gz
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| [ALL done] cpu-time used = 671.82 sec
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| [ALL done] walltime used = 114.00 sec
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| </pre>
| |
| </div>
| |
| | |
| ==Allele frequency ouput (.fopt)==
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| Each column correponds to the estimated allele frequencies for each population and each line is a SNP
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| <div class="toccolours mw-collapsible mw-collapsed">
| |
| Example of a .fopt file for -K 3
| |
| <pre class="mw-collapsible-content">
| |
| ...
| |
| 0.75331646167520038837 0.51190946588401886608 0.50134051056701267601
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| 0.99999999900000002828 0.80165850924934911603 0.97470665326916294813
| |
| 0.99999999900000002828 0.89560828888972687789 0.88062641752218895341
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| 0.99999999900000002828 0.99999999900000002828 0.86109994249930577048
| |
| 0.70560445653074521655 0.78994686954000448154 0.93076614062025020413
| |
| 0.99999999900000002828 0.88878537780630872955 0.92662857068149151463
| |
| 0.05322676762098016434 0.22871739860812340117 0.17394852600322696645
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| 0.00000000100000000000 0.27428885137150410545 0.19029599645013275944
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| 0.57086006389212373691 0.42232596591112880891 0.74080063581586474974
| |
| 0.77359733910003525281 0.47380864146016693494 0.72073560889718923939
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| 0.49946404159405927148 0.21684946347150244050 0.15201985942558055021
| |
| 0.41802171086717271331 0.55490556205954566504 0.85691127728452165524
| |
| 0.77095213528720529794 0.60074618451005279418 0.70219544996184157792
| |
| 0.26517850405564091787 0.48500265408436060710 0.85432254709914456914
| |
| 0.80055081986260245852 0.74423201242010783574 0.87110476762969968334
| |
| 0.30563054476851375663 0.05233529475348827620 0.25911912824038613179
| |
| 0.51084997710733415222 0.62263692178557350498 0.50738250264097506381
| |
| 0.64790272562679740442 0.91230541484222271720 0.73015721390331478347
| |
| 0.07124629651164265942 0.37896482494356753534 0.29218012479334326548
| |
| 0.00000000100000000000 0.26969100790961914038 0.28395781874856029781
| |
| 0.97074775756045073027 0.79093498372643300520 0.64006920058897498471
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| 0.64661948716978157048 0.84130009558421925409 0.76730057769159087933
| |
| 0.86990900887920663553 0.79410745692063922085 0.69416721874359499367
| |
| 0.34956069940263900797 0.27773038429396151860 0.25923476721423144298
| |
| 0.77739744690560164120 0.51272232330145017798 0.53888718200036844763
| |
| 0.35431569298041332150 0.20022780744715171219 0.43176580786072032980
| |
| 0.91858160919413811563 0.99999999900000002828 0.93584179237779097082
| |
| 0.90339823126358831384 0.94729687041528465308 0.84358671720630329371
| |
| 0.87068129661127857677 0.65267891763324525911 0.59315740612546075106
| |
| 0.24102496839012735319 0.42777100607917967201 0.39594098602469629533
| |
| 0.99999999900000002828 0.99999999900000002828 0.78549330115836857313
| |
| 0.15386277372522660922 0.18035502891341426146 0.26583557049163752950
| |
| 0.22456748943597096280 0.25110807159057474403 0.17244618960511531869
| |
| 0.74816053649164548922 0.54769319158907958656 0.44532166240679449398
| |
| 0.76350303696805599252 0.86547244122202959815 0.94111974586621383043
| |
| 0.40940400475566068872 0.67767095908245833513 0.40793761498610620064
| |
| 0.85389765162910868934 0.78901563183853873351 0.93614065916219291186
| |
| 0.54108661985898742763 0.61895909938546000983 0.88522763262549941654
| |
| 0.99051495581855464323 0.78855843624128341141 0.77646441702623147929
| |
| 0.51133721761171413434 0.74521610846562824637 0.32689774480116673416
| |
| 0.66618479413060949224 0.67891474309775079465 0.80762116232856140385
| |
| 0.81793598261160704865 0.77752326447671193943 0.95349025244041396565
| |
| 0.82120324647844433752 0.99999999900000002828 0.89800731971059466474
| |
| ...
| |
| </pre>
| |
| </div>
| |
| Use the -printInfo option to get the position of the lines in the fopt file if some sites have been flltered from the analysis (-minMaf, minInd, minLRT etc)
| |
| | |
| ==Admixture proportion output file (-qopt)==
| |
| Infered admixture proporsions. Each line is an individual and each column is a population.
| |
| <div class="toccolours mw-collapsible mw-collapsed">
| |
| Contents of the qopt file # cat tsk48GL.beagle.gz.s1.qopt
| |
| <pre class="mw-collapsible-content">
| |
| 0.00254460532103031574 0.00108987228478324210 0.99636552239418640919
| |
| 0.00000015905647541105 0.00000000100000000000 0.99999983994352459327
| |
| 0.00034770382567266174 0.02639209238328452459 0.97326020379104283275
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999800000005656
| |
| 0.00000467398081877176 0.00000000100000000000 0.99999532501918120264
| |
| 0.00000000907496942853 0.00585150933779484805 0.99414848158723567728
| |
| 0.00515826525767644137 0.01138897436535154552 0.98345276037697204607
| |
| 0.03914841746468285949 0.00000000100000000000 0.96085158153531713410
| |
| 0.00000000100000000000 0.00629199375758324100 0.99370800524241675866
| |
| 0.00771173022930659625 0.00000154720357311662 0.99228672256712036059
| |
| 0.00000000100000000000 0.00075135345721917719 0.99924864554278081119
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999799999994554
| |
| 0.00000005468413042120 0.00087279924180633879 0.99912714607406327705
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999800000005656
| |
| 0.00712941313019542066 0.00118955677574110528 0.99168103009406338710
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999799999994554
| |
| 0.00000000100000000000 0.00165385222968000606 0.99834614677032007535
| |
| 0.00000000100000000000 0.00006297763597355473 0.99993702136402651259
| |
| 0.00519087111391381209 0.00000000100000000000 0.99480912788608621966
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999800000005656
| |
| 0.00202872783596746379 0.00000000100000000000 0.99797127116403261393
| |
| 0.00876424336999809782 0.00949457841911990376 0.98174117821088191516
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999799999994554
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999799999994554
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999799999994554
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999799999994554
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999800000005656
| |
| 0.01820430093358888640 0.00000694033297829119 0.98178875873343274261
| |
| 0.00351013812443964728 0.00000020340562512923 0.99648965846993520223
| |
| 0.00771897550085272680 0.00605259705033356268 0.98622842744881378252
| |
| 0.00600595292580561029 0.00000000100000000000 0.99399404607419439284
| |
| 0.01454910070242997067 0.00543457657939076105 0.98001632271817917808
| |
| 0.02567862615486414535 0.00160921436783232220 0.97271215947730349516
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999800000005656
| |
| 0.00000000100000000000 0.00001041560507852223 0.99998958339492149960
| |
| 0.00000000100000000000 0.01383432553657116572 0.98616567346342876021
| |
| 0.00343840097404925389 0.00000000100000000000 0.99656159802595079000
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999800000005656
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999800000005656
| |
| 0.00051244065751142103 0.00404846039501185508 0.99543909894747661937
| |
| 0.02003953974792894652 0.00000004934009128878 0.97996041091197982897
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999799999994554
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999799999994554
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999800000005656
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999799999994554
| |
| 0.02176809890633762956 0.00000000100000000000 0.97823190009366245423
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999800000005656
| |
| 0.01563096189267457192 0.00970868396771427770 0.97466035413961116252
| |
| 0.00000000100000000000 0.00000000100000000000 0.99999999800000005656
| |
| 0.00002540964943070735 0.00000000100000000000 0.99997458935056915408
| |
| 0.99999999799999994554 0.00000000100000000000 0.00000000100000000000
| |
| 0.99501476026684787524 0.00000000100000000000 0.00498523873315206718
| |
| 0.99999999799999994554 0.00000000100000000000 0.00000000100000000000
| |
| 0.99520671498720802983 0.00479241730266987201 0.00000086771012207898
| |
| 0.95884374919730619435 0.00000000100000000000 0.04115624980269377842
| |
| 0.99002104218586972628 0.00000000100000000000 0.00997895681413022567
| |
| 0.99999999799999994554 0.00000000100000000000 0.00000000100000000000
| |
| 0.99999999800000005656 0.00000000100000000000 0.00000000100000000000
| |
| 0.99999999770925251941 0.00000000129074746013 0.00000000100000000000
| |
| 0.99999999799999994554 0.00000000100000000000 0.00000000100000000000
| |
| 0.99999999799999994554 0.00000000100000000000 0.00000000100000000000
| |
| 0.99999999800000005656 0.00000000100000000000 0.00000000100000000000
| |
| 0.99999999800000005656 0.00000000100000000000 0.00000000100000000000
| |
| 0.98980053177767901573 0.00000005577971952226 0.01019941244260143612
| |
| 0.99999999800000005656 0.00000000100000000000 0.00000000100000000000
| |
| 0.99999785004878083416 0.00000000100000000000 0.00000214895121910354
| |
| 0.99999999800000005656 0.00000000100000000000 0.00000000100000000000
| |
| 0.99999999800000005656 0.00000000100000000000 0.00000000100000000000
| |
| 0.99220030909132039820 0.00000000100000000000 0.00779968990867968733
| |
| 0.99999996788621803301 0.00000000100000000000 0.00000003111378189772
| |
| 0.99736783433174225344 0.00255940950853666971 0.00007275615972113173
| |
| 0.99998096423035520708 0.00000000574461213317 0.00001903002503262207
| |
| 0.99711097909957713270 0.00288887008493822353 0.00000015081548462101
| |
| 0.99999999799999994554 0.00000000100000000000 0.00000000100000000000
| |
| 0.99999999800000005656 0.00000000100000000000 0.00000000100000000000
| |
| 0.99999999800000005656 0.00000000100000000000 0.00000000100000000000
| |
| 0.99769262012085335734 0.00000000100000000000 0.00230737887914652393
| |
| 0.99999820787375570674 0.00000000433914936351 0.00000178778709493472
| |
| 0.98047422489554170166 0.00012980111977614777 0.01939597398468214523
| |
| 0.99999999799999994554 0.00000000100000000000 0.00000000100000000000
| |
| 0.98208006049140339488 0.00000000100000000000 0.01791993850859651197
| |
| 0.97530298545159921364 0.00000000100000000000 0.02469701354840085974
| |
| 0.99657542812406740840 0.00000000100000000000 0.00342457087593254226
| |
| 0.99954556420189066834 0.00045443479810919004 0.00000000100000000000
| |
| 0.99999999800000005656 0.00000000100000000000 0.00000000100000000000
| |
| 0.99531584565237773976 0.00410740812985130408 0.00057674621777084644
| |
| 0.99999999800000005656 0.00000000100000000000 0.00000000100000000000
| |
| 0.99878572597704817770 0.00000000100000000000 0.00121427302295177490
| |
| 0.98571687209123504125 0.00400077401169816448 0.01028235389706666329
| |
| 0.99027397554762419674 0.00840892511494516215 0.00131709933743062008
| |
| 0.99999993504923445631 0.00000000100000000000 0.00000006395076564386
| |
| 0.95946639819101930957 0.00000000100000000000 0.04053360080898076034
| |
| 0.99999999800000005656 0.00000000100000000000 0.00000000100000000000
| |
| 0.98414939425022363029 0.01585059024074651421 0.00000001550902978739
| |
| 0.99999999622245250297 0.00000000277754757396 0.00000000100000000000
| |
| 0.99525652466242930938 0.00000001683386219288 0.00474345850370842034
| |
| 0.99999999799999994554 0.00000000100000000000 0.00000000100000000000
| |
| 0.99999999799999994554 0.00000000100000000000 0.00000000100000000000
| |
| 0.99999965447943561792 0.00000000100000000000 0.00000034452056438734
| |
| 0.99864814059528783652 0.00135185840471215468 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999800000005656 0.00000000100000000000
| |
| 0.00000001076370464123 0.99999998823629543399 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000099999999999 0.99999999799999994554 0.00000000099999999999
| |
| 0.00000000099999999999 0.99999999799999994554 0.00000000099999999999
| |
| 0.00000000100000000000 0.99999999800000005656 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999800000005656 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000099999999999 0.99999999799999994554 0.00000000099999999999
| |
| 0.00000000099999999999 0.99999999800000005656 0.00000000099999999999
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000099999999999 0.99999999800000005656 0.00000000099999999999
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000099999999999 0.99999999800000005656 0.00000000099999999999
| |
| 0.00000000100000000000 0.99999999800000005656 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999800000005656 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000099999999999 0.99999999800000005656 0.00000000099999999999
| |
| 0.00000000099999999999 0.99999999800000005656 0.00000000099999999999
| |
| 0.00000000099999999999 0.99999999799999994554 0.00000000099999999999
| |
| 0.00000000099999999999 0.99999999799999994554 0.00000000099999999999
| |
| 0.00000000099999999999 0.99999999800000005656 0.00000000099999999999
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999800000005656 0.00000000100000000000
| |
| 0.00000000099999999999 0.99999999799999994554 0.00000000099999999999
| |
| 0.00000000099999999999 0.99999999799999994554 0.00000000099999999999
| |
| 0.00000000099999999999 0.99999999799999994554 0.00000000099999999999
| |
| 0.00000000100000000000 0.99999999800000005656 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999800000005656 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999800000005656 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999800000005656 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999800000005656 0.00000000100000000000
| |
| 0.00000000099999999999 0.99999999799999994554 0.00000000099999999999
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999999800000005656 0.00000000100000000000
| |
| 0.00000000100000000000 0.99999986659623718577 0.00000013240376283687
| |
| 0.00000000099999999999 0.99999999799999994554 0.00000000099999999999
| |
| 0.00000000099999999999 0.99999999799999994554 0.00000000099999999999
| |
| 0.00000000100000000000 0.99632783404679736705 0.00367216495320256799
| |
| 0.00000000100000000000 0.99999999799999994554 0.00000000100000000000
| |
| 0.00000000099999999999 0.99999999800000005656 0.00000000099999999999
| |
| 0.35919621347731411909 0.32381633362411937904 0.31698745289856661289
| |
| 0.31048363757756514136 0.30902410742704566893 0.38049225499538924522
| |
| 0.36341140678787386964 0.33678307361394943520 0.29980551959817652863
| |
| 0.34550713774447228133 0.34037087985425079628 0.31412198240127681137
| |
| 0.34705579219215104692 0.35218792485566730033 0.30075628295218165276
| |
| 0.33646039412306782967 0.32632754139618752598 0.33721206448074481088
| |
| 0.31881401220765009930 0.34885621407165418040 0.33232977372069577582
| |
| 0.34999374672052624424 0.33030931848049555066 0.31969693479897826061
| |
| 0.33152251818028721786 0.32339147992992234304 0.34508600188979043910
| |
| 0.31959998197389311025 0.33152491237148390413 0.34887510565462298562
| |
| 0.34724548642936803322 0.31809475756470984020 0.33465975600592196004
| |
| 0.33378069767858009609 0.33223636639277298599 0.33398293592864686241
| |
| 0.32023090400419051971 0.33179989332826043125 0.34796920266754916007
| |
| 0.35205158009776410521 0.33547091017851976558 0.31247750972371612921
| |
| 0.34291063455495451873 0.31853488093100223999 0.33855448451404313026
| |
| 0.31929132670383747472 0.32755905579808902717 0.35314961749807355362
| |
| 0.34114474726121107873 0.34607065583774476725 0.31278459690104404300
| |
| 0.33725705347681012025 0.32910919226619778089 0.33363375425699209886
| |
| 0.33918213722968154622 0.32278745806952213737 0.33803040470079642743
| |
| 0.33788659799509024317 0.34692305448657090317 0.31519034751833896468
| |
| 0.35876135180876589370 0.33843260979944000955 0.30280603839179404124
| |
| 0.34721570614318736370 0.34395335873604998556 0.30883093512076259524
| |
| 0.34165097731337079612 0.32814110943000784903 0.33020791325662146587
| |
| 0.33922542743931027864 0.32639619830977489867 0.33437837425091476717
| |
| 0.34461619391735059947 0.33133174331942943924 0.32405206276321996128
| |
| 0.34277551565686120716 0.32746953398981676342 0.32975495035332202942
| |
| 0.33842982221926010133 0.31224638933762871584 0.34932378844311123833
| |
| 0.34443810815667752490 0.32640113997211872565 0.32916075187120380496
| |
| 0.31723258569943768581 0.34955203711397470068 0.33321537718658750249
| |
| 0.35394053250677920408 0.33291498389624818444 0.31314448359697255597
| |
| 0.33504517457864940733 0.34188143503173562543 0.32307339038961496724
| |
| 0.33240938202788244960 0.34671459781042585080 0.32087602016169164409
| |
| 0.31745792352948248860 0.33722730677636020280 0.34531476969415725309
| |
| 0.33098224522913716195 0.33312298285105168549 0.33589477191981131909
| |
| 0.34090909280056919117 0.32423671881295645925 0.33485418838647434958
| |
| 0.32985465610121944557 0.32124851771265583444 0.34889682618612483100
| |
| 0.33525528582568764335 0.31967441393853385234 0.34507030023577844879
| |
| 0.33823045943274382408 0.33932114218381809190 0.32244839838343819505
| |
| 0.34374166546335593875 0.33527470302709477812 0.32098363150954922762
| |
| 0.32177399566214615056 0.34277626859597382092 0.33544973574188002852
| |
| 0.34915111840878915173 0.33072079898488659921 0.32012808260632419355
| |
| 0.31132788816691708833 0.32844185942225745389 0.36023025241082540227
| |
| 0.33067206673512555826 0.34601992411426535368 0.32330800915060908807
| |
| 0.31337643746173032833 0.33835721859074846529 0.34826634394752131740
| |
| 0.32762993090356395953 0.34856645453438306337 0.32380361456205303261
| |
| 0.33558678075595765877 0.34449062515269568419 0.31992259409134682357
| |
| 0.33433652456352996873 0.32868556951924504661 0.33697790591722515119
| |
| 0.32115036446030281736 0.35050069566489522321 0.32834893987480190392
| |
| 0.32524569843140932468 0.33953480032298033464 0.33521950124561045170
| |
| 0.33520046917246110185 0.31124301814705779279 0.35355651268048110536
| |
| 0.51565151014669796670 0.00027180960956305278 0.48407668024373901039
| |
| 0.51978922685130035664 0.01333903580405943964 0.46687173734464021413
| |
| 0.48123878312258933088 0.00648941795451128591 0.51227179892289931296
| |
| 0.48941833241028537271 0.00512373007237581363 0.50545793751733880672
| |
| 0.48421136927686320162 0.00600153379448644612 0.50978709692865020742
| |
| 0.53246468447754891073 0.00000000100000000000 0.46753531452245111755
| |
| 0.50637710620505416159 0.01564455874020675985 0.47797833505473913407
| |
| 0.49416813414210103428 0.00000000100000000000 0.50583186485789899400
| |
| 0.51328206693115174808 0.00000000100000000000 0.48671793206884833571
| |
| 0.50420356848059588728 0.00779539942445491366 0.48800103209494921641
| |
| 0.51589943710654184716 0.00000000100000000000 0.48410056189345807010
| |
| 0.46643393286795947761 0.00024627960390510270 0.53331978752813535838
| |
| 0.50134326603627110686 0.00000000100000000000 0.49865673296372897694
| |
| 0.52516062216154979492 0.00887494007947397384 0.46596443775897622430
| |
| 0.50553300231497877437 0.00610541400596737328 0.48836158367905380118
| |
| 0.48505848053244243756 0.00412236953776635561 0.51081914992979127188
| |
| 0.50419106430093152404 0.00671707921410998055 0.48909185648495850929
| |
| 0.51266037905765671212 0.00565931340437971983 0.48168030753796364785
| |
| 0.50479638826213368841 0.00082364200405335279 0.49437996973381287402
| |
| 0.48963785250324892706 0.00000000100000000000 0.51036214649675115673
| |
| 0.49861342640726780129 0.00000000100000000000 0.50138657259273211597
| |
| 0.49321745088202589846 0.00000000100000000000 0.50678254811797418533
| |
| 0.52297921048641760056 0.00000000100000000000 0.47702078851358242773
| |
| 0.51351947193443381323 0.00000000100000000000 0.48648052706556610403
| |
| 0.49861600587139209839 0.01143470350387426789 0.48994929062473369097
| |
| 0.47497824395255133778 0.00413641430709298184 0.52088534174035572288
| |
| 0.50602874958787047444 0.00000013752429825494 0.49397111288783129845
| |
| 0.51347175918678078510 0.00477133273041653854 0.48175690808280269284
| |
| 0.50359809216181616875 0.00000002299679746021 0.49640188484138642044
| |
| 0.52201190781479689385 0.00000000100000000000 0.47798809118520296790
| |
| 0.52427554763933403859 0.01637369304678280152 0.45935075931388308357
| |
| 0.50464335890649447691 0.01062810063722730188 0.48472854045627822295
| |
| 0.48795095623978190780 0.00032508303858300066 0.51172396072163517378
| |
| 0.49273360783177866384 0.03185613233234574349 0.47541025983587564818
| |
| 0.49075081269029041664 0.00043182816413278401 0.50881735914557668643
| |
| 0.51236233643387329995 0.01050799870797843559 0.47712966485814828355
| |
| 0.51939186110717183720 0.00638063180499700081 0.47422750708783106832
| |
| 0.49685157861691658931 0.00000000100000000000 0.50314842038308338346
| |
| 0.50376251978896124939 0.00609062514993390959 0.49014685506110500235
| |
| 0.50469879197514677660 0.00000000100000000000 0.49530120702485330719
| |
| 0.48806858812981018803 0.00000000100000000000 0.51193141087018978475
| |
| 0.49345173654735252633 0.00767168036095551131 0.49887658309169191639
| |
| 0.51926063211476558568 0.00000000100000000000 0.48073936688523438709
| |
| 0.49182360714466144547 0.00000000100000000000 0.50817639185533869384
| |
| 0.50012065040991493525 0.00101172020552988784 0.49886762938455525562
| |
| 0.49490771372946151807 0.00000000100000000000 0.50509228527053839919
| |
| 0.50981594186492362741 0.01168450085559137597 0.47849955727948501050
| |
| 0.48459184220397827358 0.00000007440008454733 0.51540808339593724430
| |
| 0.51153925961371649045 0.00045999176804108893 0.48800074861824249695
| |
| 0.49380129779182529992 0.00214174101547949525 0.50405696119269527422
| |
| 0.10504303642339951619 0.45848347542219436423 0.43647348815440606407
| |
| 0.09383999674587484296 0.44580529318052469767 0.46035471007360045936
| |
| 0.11801124345951279071 0.44619343422410290279 0.43579532231638429263
| |
| 0.10150817897299509174 0.44474184109029252232 0.45374997993671234431
| |
| 0.14144944553914898244 0.47426718065022838156 0.38428337381062249722
| |
| 0.08656596263718574491 0.47201374694852676894 0.44142029041428754166
| |
| 0.10422682420288104099 0.45665008652196642513 0.43912308927515242285
| |
| 0.07422281507005458467 0.46668026430253822801 0.45909692062740725671
| |
| 0.11152984148911383733 0.44326164444242566187 0.44520851406846068121
| |
| 0.12101900721666984662 0.45534926548479054409 0.42363172729853953991
| |
| 0.19287147372937366030 0.40220634979635128126 0.40492217647427497518
| |
| 0.19868166550667537562 0.39952077624337684059 0.40179755824994778379
| |
| 0.20144056442189406386 0.40552701281654912613 0.39303242276155692103
| |
| 0.17400131741109717276 0.41572345587205422612 0.41027522671684846234
| |
| 0.19363830614785534912 0.39941552029693161430 0.40694617355521295332
| |
| 0.20932370419936904837 0.41063785306931777086 0.38003844273131326403
| |
| 0.21496306930156286463 0.41077627378883840858 0.37426065690959875454
| |
| 0.20887311245081657818 0.39219787302656328176 0.39892901452262014006
| |
| 0.18789467459437667052 0.42880445734573224836 0.38330086805989094234
| |
| 0.21467435158258502126 0.41396326091136687042 0.37136238750604805281
| |
| 0.30215275924600598634 0.35114326369103593395 0.34670397706295807971
| |
| 0.27985580964526363124 0.36766711333486662427 0.35247707701986974449
| |
| 0.29214764907998119758 0.34353124024041165052 0.36432111067960715189
| |
| 0.28098186396660507214 0.35436535705487937076 0.36465277897851555711
| |
| 0.29909659519210785028 0.34708664349540557792 0.35381676131248662731
| |
| 0.29960230758566036569 0.34764467237891033546 0.35275302003542929885
| |
| 0.28690707484319816212 0.36958476358894237768 0.34350816156785934918
| |
| 0.31218824558522878521 0.35988855578362860532 0.32792319863114272049
| |
| 0.29371283648699086921 0.34536893102077848017 0.36091823249223065062
| |
| 0.32028624797598659324 0.35059182523172049972 0.32912192679229296255
| |
| 0.39315538655109805166 0.30778919233772789044 0.29905542111117405790
| |
| 0.39625700997625840083 0.29350948690034872612 0.31023350312339292856
| |
| 0.40087160410050781678 0.31851581382017457589 0.28061258207931755182
| |
| 0.40117357253398744366 0.30569836130272198815 0.29312806616329067921
| |
| 0.40013703551439627759 0.28691859513594913933 0.31294436934965452757
| |
| 0.39131222513930874474 0.30759794867682349606 0.30108982618386764818
| |
| 0.40826221599444090238 0.30658973748486684219 0.28514804652069231095
| |
| 0.41420080477834714250 0.28227625784283560950 0.30352293737881719249
| |
| 0.39119930707342420728 0.32102763805993583812 0.28777305486664006562
| |
| 0.37635520411942069430 0.29805329179310008358 0.32559150408747933314
| |
| 0.51400585200303006150 0.26100245041580294458 0.22499169758116702167
| |
| 0.50336119658518030384 0.25110166586697690860 0.24553713754784287082
| |
| 0.47299237773462793344 0.26084178003823194070 0.26616584222714018138
| |
| 0.49359314224598493936 0.26013978211456978418 0.24626707563944530421
| |
| 0.52795469779405246324 0.26499345968140075591 0.20705184252454675309
| |
| 0.48219467330650939152 0.25987283477635270135 0.25793249191713785162
| |
| 0.47626160019217189667 0.25351817092177358903 0.27022022888605456981
| |
| 0.51617477226059282902 0.23162353057460718930 0.25220169716479995392
| |
| 0.49698887507445854705 0.24557159475841641716 0.25743953016712495252
| |
| 0.52733914260860248469 0.25309832534801629533 0.21956253204338116447
| |
| 0.56749881833694781896 0.19172441472755546998 0.24077676693549673881
| |
| 0.59339160859286765870 0.19241414198845174788 0.21419424941868048240
| |
| 0.62308540846251914136 0.18054125203843729430 0.19637333949904353658
| |
| 0.59485531592769125275 0.20909554531024135415 0.19604913876206744860
| |
| 0.61310545246842529377 0.20645329445333451823 0.18044125307824007698
| |
| 0.60102956519838679483 0.21237444166376903687 0.18659599313784405727
| |
| 0.59278179178128642679 0.20826418834431797977 0.19895401987439562119
| |
| 0.60456224253100432353 0.20686687908046738626 0.18857087838852840123
| |
| 0.59417710257213784963 0.21264514488765640099 0.19317775254020574938
| |
| 0.59059286756608764257 0.21451811369415349495 0.19488901873975889023
| |
| 0.69484036887292865980 0.14634823390637874407 0.15881139722069256837
| |
| 0.69945423984127830241 0.16333221995631252987 0.13721354020240922322
| |
| 0.69115689116107958956 0.14927316115273414621 0.15956994768618620872
| |
| 0.68851717088680941536 0.14201541767923545057 0.16946741143395496754
| |
| 0.69288781352263861812 0.14270021794166909412 0.16441196853569234326
| |
| 0.68819873910998985433 0.16242980538224471854 0.14937145550776548264
| |
| 0.68619763716276405141 0.14370194479775053042 0.17010041803948539041
| |
| 0.68596343194490616568 0.16051691534743553480 0.15351965270765843830
| |
| 0.70684340251150390433 0.16654037983665334610 0.12661621765184280508
| |
| 0.70657158115262697073 0.14984891346689468983 0.14357950538047842270
| |
| 0.79161214498168253062 0.10430887542937690438 0.10407897958894059276
| |
| 0.79477141808375573184 0.10274451187208989700 0.10248407004415439892
| |
| 0.80425538032447896342 0.10720945367236509038 0.08853516600315590457
| |
| 0.79445836435866723502 0.11481368508653701233 0.09072795055479568327
| |
| 0.80626524450581027459 0.08599284906042292675 0.10774190643376663212
| |
| 0.77991736902186048486 0.08777798585427237787 0.13230464512386716502
| |
| 0.77897241390666871474 0.11419808069913564563 0.10682950539419577840
| |
| 0.80225596727756287585 0.10739115862914316857 0.09035287409329402497
| |
| 0.81035643868218754093 0.11405964018980654928 0.07558392112800596530
| |
| 0.80474324803558927588 0.09992219310105134034 0.09533455886335934215
| |
| 0.89147290804053958002 0.05818869713285088757 0.05033839482660958098
| |
| 0.87135519951168793895 0.04885203404408157424 0.07979276644423052844
| |
| 0.90273220877706750187 0.05642671780738096193 0.04084107341555152232
| |
| 0.90299890240805003039 0.05982401615206547896 0.03717708143988454617
| |
| 0.88622329583732417646 0.03227381365259313073 0.08150289051008267893
| |
| 0.89149278212958615875 0.03556871666107842139 0.07293850120933542680
| |
| 0.90540444756330573650 0.06637446770308205735 0.02822108473361228942
| |
| 0.89581315874618450135 0.06675457610008654619 0.03743226515372900798
| |
| 0.86941364504212315101 0.03330392614486758773 0.09728242881300920575
| |
| 0.88098981477392690476 0.04673780362475228600 0.07227238160132080924
| |
| </pre>
| |
| </div>
| |
| | |
| =Plot results=
| |
| plot in the order of the input file
| |
| <pre>
| |
| admix<-t(as.matrix(read.table("myoutfiles.qopt")))
| |
| barplot(admix,col=1:3,space=0,border=NA,xlab="Individuals",ylab="admixture")
| |
| </pre>
| |
| [[File:NGSadmixEx1.png|frameless|600px]]
| |
| | |
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| plot using a population label file
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| <pre>
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| pop<-read.table("pop.info",as.is=T)
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| admix<-t(as.matrix(read.table("myoutfiles.qopt")))
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| admix<-admix[,order(pop[,1])]
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| pop<-pop[order(pop[,1]),]
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| h<-barplot(admix,col=1:3,space=0,border=NA,xlab="Individuals",ylab="admixture")
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| text(tapply(1:nrow(pop),pop[,1],mean),-0.05,unique(pop[,1]),xpd=T)
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| </pre>
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| [[File:NGSadmixEx2.png|frameless|600px]]
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| =citation=
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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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