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| This page contains information about the program called NGSadmix, which is a very nice tool for finding admixture proportions from NGS data. 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. We really like it.
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| [[File:NgsAdmix.png|thumb]]
| | The software including tutorials can be found here |
| Latest version is 32 from June 25 2013. It can be found [http://popgen.dk/software/download/NGSadmix/ngsadmix32.cpp ]. Older versions can be found here:
| | https://github.com/aalbrechtsen/NGSadmix |
| [http://popgen.dk/software/download/NGSadmix/].
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| | |
| Method is published and can be found here: [http://www.ncbi.nlm.nih.gov/pubmed/24026093]
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| =Installation=
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| | |
| <pre>
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| wget popgen.dk/software/download/NGSadmix/ngsadmix32.cpp
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| g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix
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| </pre>
| |
| | |
| =Brief Overview=
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| <div class="toccolours mw-collapsible mw-collapsed">
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| ./NGSadmix
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| <pre class="mw-collapsible-content">
| |
| 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>
| |
| </div>
| |
| NB All parameters are set using '''-par value'''. So to get additional information you would write '''-printInfo 1'''.
| |
| | |
| =Run example=
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| First download some example test files which has been generated on basis of data from the 1000 genomes project (100 individuals from 5 populations with 50000 SNPs).
| |
| <pre>
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| wget popgen.dk/software/download/NGSadmix/data/input.gz
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| wget popgen.dk/software/download/NGSadmix/data/pop.info
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| </pre>
| |
| | |
| We then have an input file called input.gz and assuming 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).
| |
| | |
| <div class="toccolours mw-collapsible mw-collapsed">
| |
| ./NGSadmix -likes input.gz -K 3 -P 4 -o myoutfiles -minMaf 0.05
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| <pre class="mw-collapsible-content">
| |
| -> Dumping file: myoutfiles.log
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| -> Dumping file: myoutfiles.filter
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| Input: lname=input.gz nPop=3, fname=(null) qname=(null) outfiles=myoutfiles
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| Setup: seed=1374071670 nThreads=4 method=1
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| Convergence: maxIter=2000 tol=0.000010 tolLike50=0.100000 dymBound=0
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| Filters: misTol=0.050000 minMaf=0.050000 minLrt=0.000000 minInd=0
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| Input file has dim: nsites=50000 nind=100
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| Input file has dim (AFTER filtering): nsites=49475 nind=100
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| iter[start] like is=6395247.407627
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| iter[50] like is=-3868746.751237 thres=0.002523
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| iter[100] like is=-3866294.760777 thres=0.003179
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| iter[150] like is=-3865984.169517 thres=0.000310
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| iter[200] like is=-3865965.879519 thres=0.000017
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| EM accelerated Thread has reached convergence with tol 0.000010
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| best like=-3865964.425455 after 245 iterations
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| -> Dumping file: myoutfiles.qopt
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| -> Dumping file: myoutfiles.fopt.gz
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| [ALL done] cpu-time used = 211.93 sec
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| [ALL done] walltime used = 105.00 sec
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| | |
| </pre>
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| </div>
| |
| | |
| =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. See [http://www.popgen.dk/angsd/index.php/Beagle_input Creation of Beagle files with ANGSD]
| |
| | |
| Example of a beagle genotype likelihood input file for 3 individuals.
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| <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 and can contain whatever dummy value).
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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.
| |
| | |
| The input file is allowed to be compressed with gzip.
| |
| | |
| =Options=
| |
| <pre>
| |
| ./NGSadmix
| |
| 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
| |
| 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:
| |
| -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=
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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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| | |
| * 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.
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| | |
| | |
| ==Log file (.log)==
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| <div class="toccolours mw-collapsible mw-collapsed">
| |
| Contents of the file log file
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| <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
| |
| </pre>
| |
| </div>
| |
| | |
| ==Allele frequency ouput (.fopt)==
| |
| 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
| |
| 0.99999999900000002828 0.80165850924934911603 0.97470665326916294813
| |
| 0.99999999900000002828 0.89560828888972687789 0.88062641752218895341
| |
| 0.99999999900000002828 0.99999999900000002828 0.86109994249930577048
| |
| 0.70560445653074521655 0.78994686954000448154 0.93076614062025020413
| |
| 0.99999999900000002828 0.88878537780630872955 0.92662857068149151463
| |
| 0.05322676762098016434 0.22871739860812340117 0.17394852600322696645
| |
| 0.00000000100000000000 0.27428885137150410545 0.19029599645013275944
| |
| 0.57086006389212373691 0.42232596591112880891 0.74080063581586474974
| |
| 0.77359733910003525281 0.47380864146016693494 0.72073560889718923939
| |
| 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
| |
| 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
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| 0.82120324647844433752 0.99999999900000002828 0.89800731971059466474
| |
| ...
| |
| </pre>
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| </div>
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| Use the "-printInfo 1" 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)
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| | |
| ==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
| |
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| 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]]
| |
| | |
| | |
| Plot using a population label file.
| |
| <pre>
| |
| pop<-read.table("pop.info",as.is=T)
| |
| admix<-t(as.matrix(read.table("myoutfiles.qopt")))
| |
| admix<-admix[,order(pop[,1])]
| |
| pop<-pop[order(pop[,1]),]
| |
| h<-barplot(admix,col=1:3,space=0,border=NA,xlab="Individuals",ylab="admixture")
| |
| text(tapply(1:nrow(pop),pop[,1],mean),-0.05,unique(pop[,1]),xpd=T)
| |
| </pre>
| |
| [[File:NGSadmixEx2.png|frameless|600px]]
| |
| | |
| =Citation=
| |
| http://www.genetics.org/content/early/2013/09/03/genetics.113.154138.full.pdf
| |
| ==Bibtex==
| |
| <pre>
| |
| % 24026093
| |
| @Article{pmid24026093,
| |
| Author="Skotte, L. and Korneliussen, T. S. and Albrechtsen, A. ",
| |
| Title="{{E}stimating {I}ndividual {A}dmixture {P}roportions from {N}ext {G}eneration {S}equencing {D}ata}",
| |
| Journal="Genetics",
| |
| Year="2013",
| |
| Pages=" ",
| |
| Month="Sep"
| |
| }
| |
| </pre>
| |
| | |
| =Log=
| |
| * v32 june 25-2013; modified code such that it now compiles on OSX
| |
| * v31 june 24-2013; First public version.
| |