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| The great thing about NGSadmix is that it is a new method that takes the uncertainty introduced in NGS sequencing data into account when inferring an individual's ancestry by using genotype likelihoods that considers the uncertainty caused by unobserved genotypes. | | The great thing about NGSadmix is that it is a new method that takes the uncertainty introduced in NGS sequencing data into account when inferring an individual's ancestry by using genotype likelihoods that considers the uncertainty caused by unobserved genotypes. |
| | |
| | As with the other existing software, ADMIXTURE and STRUCTURE, NGSadmix is only sensitive to admixture recent enough to cause structures in the population in terms of differing allele frequencies. Historical admixture events after which many generations has passed in the population, leaves no signature in terms of systematic differences in allele frequencies between individuals and are not a concern in association studies. |
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| [[File:NgsAdmix.png|thumb]] | | [[File:NgsAdmix.png|thumb]] |
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| The method was published in 2013 and can be found here: [http://www.ncbi.nlm.nih.gov/pubmed/24026093] | | The method was published in 2013 and can be found here: [http://www.ncbi.nlm.nih.gov/pubmed/24026093] |
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| =Citation=
| |
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| http://www.genetics.org/content/early/2013/09/03/genetics.113.154138.full.pdf | | ==Software Download== |
| | The latest version of NGSadmix is ngsadmix32 from June 25, 2013 and can be downloaded here: [http://popgen.dk/software/download/NGSadmix/ngsadmix32.cpp]. |
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| Skotte, L., Korneliussen, T. S., & Albrechtsen, A. (2013). Estimating individual admixture proportions from next generation sequencing data. Genetics, 195(3), 693–702. doi:10.1534/genetics.113.154138
| | :'''Older Versions''' |
| | :The previous version of NGSadmix, ngsadmix31 can be found here: [http://popgen.dk/software/download/NGSadmix/ngsadmix31.cpp]. |
| | :Version Log: |
| | :* v32 june 25-2013; modified code such that it now compiles on OSX |
| | :* v31 june 24-2013; First public version. |
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| |
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| ==Bibtex== | | ==Installation== |
| <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",
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| Year="2013",
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| Pages=" ",
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| Month="Sep"
| |
| }
| |
| </pre>
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| | NGSadmix can be installed independently or as a part of ANGSD. |
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| =Download= | | ====NGSadmix Independent Installation==== |
| The latest version is 32 from June 25 2013 and can be downloaded here: [http://popgen.dk/software/download/NGSadmix/ngsadmix32.cpp].
| |
|
| |
|
| =Older Versions=
| | 1. Login to your server using ssh on your terminal window. |
| Older versions can be found here:
| |
| [http://popgen.dk/software/download/NGSadmix/].
| |
| * v32 june 25-2013; modified code such that it now compiles on OSX
| |
| * v31 june 24-2013; First public version.
| |
|
| |
|
| =Installation=
| | 2. Create the directory where you will install your software and enter it, such as |
| | :<code>mkdir ~/Software</code> |
| | :<code>cd ~/Software</code> |
|
| |
|
| <pre> | | 3. Download the source code: |
| | :<code>wget https://raw.githubusercontent.com/ANGSD/angsd/master/misc/ngsadmix32.cpp </code> |
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| |
|
| NGSadmix can be installed independently or as a part of ANGSD. | | 4. Configure, Compile and Install: |
| | :<code>g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix</code> |
|
| |
|
| 1) NGSadmix Independent Installation:
| | ====NGSadmix Installation from ANGSD==== |
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| |
|
| | :NGSadmix is part of the package ANGSD. To install ANGSD, please follow the instructions here [http://popgen.dk/angsd/index.php/Installation] |
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|
| Login to your server using ssh on your terminal window.
| | ==Parameters== |
| Create the directory where you will install your software and enter it, such as
| |
| mkdir ~/Software
| |
| cd ~/Software
| |
|
| |
|
| Download the source code:
| | All parameters are set using '''-par value'''. |
| wget https://raw.githubusercontent.com/ANGSD/angsd/master/misc/ngsadmix32.cpp
| | For example, to get additional information, you would write '''-printInfo 1'''. |
|
| |
|
| Configure, Compile and Install:
| | <pre>./NGSadmix </pre> |
| g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix
| |
|
| |
|
| Delete source code to save space:
| | Arguments: |
| rm ~/Software/ngsadmix32.cpp
| |
|
| |
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| | ::'''-likes''' .beagle format filename with genotype likelihoods |
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| | ::'''-K''' Number of ancestral populations |
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| |
|
| </pre>
| | Optional: |
|
| |
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| =Parameters=
| | ::'''-fname''' Ancestral population frequencies |
|
| |
|
| <div class="toccolours mw-collapsible mw-collapsed">
| | ::'''-qname''' Admixture proportions |
|
| |
|
| ./NGSadmix
| | ::'''-outfiles''' Prefix for output files |
| <pre class="mw-collapsible-content">
| |
|
| |
|
| *** see doc for options/possible ranges/ and further explanation
| | ::'''-printInfo''' print ID and mean maximum allele frequency (maf) for the SNPs that were analysed |
|
| |
|
| Arguments:
| |
| -likes .beagle format filename with genotype likelihoods
| |
| -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: | | 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
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| 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>
| |
| </div>
| |
| NB All parameters are set using '''-par value'''. So to get additional information you would write '''-printInfo 1'''.
| |
|
| |
|
| =Input Files=
| | ::'''-seed''' Seed for initial guess in EM algorithm (a number lower than 1M is preferred). |
| 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]
| | :: The same seed can be used to reproduce the analysis, and 3 different seeds can be used to test convergence. |
| | |
| | ::'''-P''' Number of threads |
| | |
| | ::'''-method''' 0 indicates no acceleration of EM algorithm. Please refer to the paper for more information. |
| | |
| | ::'''-misTol''' Tolerance for considering a site as missing. Default = 0.05. |
| | :: To include high quality genotypes only, increase this value (for example, 0.9) |
| | |
| | Stop criteria: |
|
| |
|
| Example of a beagle genotype likelihood input file for 3 individuals.
| | ::'''-tolLike50''' Loglikelihood difference in 50 iterations. Default= 0.1 |
| <pre>
| |
| marker allele1 allele2 Ind0 Ind0 Ind0 Ind1 Ind1 Ind1 Ind2 Ind2 Ind2
| |
| 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
| |
| ...
| |
| </pre>
| |
| Column 1:The marker name (the information is not atually used)
| |
|
| |
|
| Column 2 and 3: the major and minor allele (these two columns are not used within the program and can contain whatever dummy value).
| | ::'''-tol''' Tolerance for convergence. Default = 1x10<sup>-5</sup>. Use maller values for higher accuracy. |
| | :: It's the maximum squared difference of F and Q (please refer to the paper for formula). |
|
| |
|
| The rest of the colums are the genotypes likelihoods (not in log space). For each individual we have 3 columns.
| | ::'''-dymBound''' Use dymamic boundaries (1: yes (default) 0: no). |
| 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.
| |
|
| |
|
| | ::'''-maxiter''' Maximum number of EM iterations. Default = 2000 (high value). |
| | :: In case it doesn't converge, this value needs to be higher. |
|
| |
|
| =Output Files=
| | Filtering: |
| Program outputs 3 files.
| |
|
| |
|
| # PREFIX.log
| | ::'''-minMaf''' Minimum minor allele frequency. Default = 5% |
| # PREFIX.fopt.gz
| |
| # PREFIX.qopt
| |
|
| |
|
| * 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.
| | ::'''-minLrt''' Minimum likelihood ratio value for maf>0. Default = 0 |
|
| |
|
| * The .fopt.gz file is an compressed file, which contains an estimate of the frequency for each site for all populations.
| | ::'''-minInd''' Minumum number of informative individuals. Default = 0 |
| | :: It only keeps sites where there is at least x # of individuals with NGS data. |
|
| |
|
| * The .qopt file contains the admixture proportions for all individuals.
| | ==Input File== |
|
| |
|
| Examples of the output files are found below.
| | The input file contains genotype likelihoods in a .beagle file format [http://faculty.washington.edu/browning/beagle/beagle.html]. |
| | and can be compressed with gzip. |
| | === BAM files === |
| | If you have BAM files you can use [[ANGSD]] to produce genotype likelihoods in .beagle format. Please |
| | see [http://www.popgen.dk/angsd/index.php/Beagle_input Creation of Beagle files with ANGSD] |
|
| |
|
| | === VCF files === |
| | If you already have made a VCF file that contains genotype likehood information then it should be possible to convert .vcf files with genotype likelihoods to .beagle file via vcftools [https://vcftools.github.io/man_latest.html] |
|
| |
|
| ==Log file (.log)==
| | <pre> |
| <div class="toccolours mw-collapsible mw-collapsed">
| | vcftools --vcf input.vcf --out test --BEAGLE-GL --chr 1,2 |
| Contents of the file log file
| |
| <pre class="mw-collapsible-content"> | |
| -> 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> | | </pre> |
| </div>
| | Chromosome has to be specified. |
|
| |
|
| ==Allele frequency ouput (.fopt)==
| | You can also use bcftools' [https://samtools.github.io/bcftools/bcftools.html] 'query' option for generating a .beagle file from a .vcf file. |
| Each column correponds to the estimated allele frequencies for each population and each line is a SNP
| | |
| <div class="toccolours mw-collapsible mw-collapsed">
| | ==Output Files== |
| Example of a .fopt file for -K 3
| | The analysis performed by NGSadmix produces 4 files: |
| <pre class="mw-collapsible-content">
| | |
| ...
| | * Log likelihood of the estimates: a .log file that summarizes the run. The Command line used for running the program, what the likelihood is every 50 iterations, and finally how long it took to do the run. |
| 0.75331646167520038837 0.51190946588401886608 0.50134051056701267601
| | |
| 0.99999999900000002828 0.80165850924934911603 0.97470665326916294813
| | * Estimated allele frequency: a zipped .fopt file, that contains an estimate of the allele frequency in each of the 3 assumed ancestral populations. There is a line for each locus. |
| 0.99999999900000002828 0.89560828888972687789 0.88062641752218895341
| | |
| 0.99999999900000002828 0.99999999900000002828 0.86109994249930577048
| | * Estimated admixture proportions: a .qopt file, that contains an estimate of the individual's ancestry proportion (admixture) from each of the three assumed ancestral populations for all individuals. There is a line for each individual. |
| 0.70560445653074521655 0.78994686954000448154 0.93076614062025020413
| | |
| 0.99999999900000002828 0.88878537780630872955 0.92662857068149151463
| | ==Run command example== |
| 0.05322676762098016434 0.22871739860812340117 0.17394852600322696645
| | |
| 0.00000000100000000000 0.27428885137150410545 0.19029599645013275944
| | Download the input file, for example |
| 0.57086006389212373691 0.42232596591112880891 0.74080063581586474974
| | ::<code>wget popgen.dk/software/download/NGSadmix/data/input.gz</code> |
| 0.77359733910003525281 0.47380864146016693494 0.72073560889718923939
| | |
| 0.49946404159405927148 0.21684946347150244050 0.15201985942558055021
| | Execute NGSadmix |
| 0.41802171086717271331 0.55490556205954566504 0.85691127728452165524
| | ::<code>./NGSadmix -likes input.gz -K 3 -P 4 -o myoutfiles -minMaf 0.05</code> |
| 0.77095213528720529794 0.60074618451005279418 0.70219544996184157792
| | |
| 0.26517850405564091787 0.48500265408436060710 0.85432254709914456914
| | ::* '''-likes''' Input .beagle file of genotype likelihoods = input.gz |
| 0.80055081986260245852 0.74423201242010783574 0.87110476762969968334
| | ::* '''-K''' Ancestral populations K=3 |
| 0.30563054476851375663 0.05233529475348827620 0.25911912824038613179
| | ::* '''-P''' Number of threads used, as computer cores = 4 |
| 0.51084997710733415222 0.62263692178557350498 0.50738250264097506381
| | ::* '''-o''' Output prefix, output file names = myoutfiles |
| 0.64790272562679740442 0.91230541484222271720 0.73015721390331478347
| | ::*'''-minMaf''' SNPs with MAF > 5% = 0.05 |
| 0.07124629651164265942 0.37896482494356753534 0.29218012479334326548
| | |
| 0.00000000100000000000 0.26969100790961914038 0.28395781874856029781
| | ===Detailed Examples and Tutorial=== |
| 0.97074775756045073027 0.79093498372643300520 0.64006920058897498471
| | |
| 0.64661948716978157048 0.84130009558421925409 0.76730057769159087933
| | Please refer to the tutorial's page [http://www.popgen.dk/software/index.php/NgsAdmixTutorial] |
| 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 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)
| |
|
| |
|
| ==Admixture proportion output file (.qopt)== | | ==Citation== |
| 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
| |
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| 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>
| |
|
| |
|
| | http://www.genetics.org/content/early/2013/09/03/genetics.113.154138.full.pdf |
|
| |
|
| =Run example=
| | Skotte, L., Korneliussen, T. S., & Albrechtsen, A. (2013). Estimating individual admixture proportions from next generation sequencing data. Genetics, 195(3), 693–702. doi:10.1534/genetics.113.154138 |
|
| |
|
| Please refer to the tutorial [http://www.popgen.dk/software/index.php/NgsAdmixTutorial]
| | :<u>'''Bibtex'''</u> |
| | :% 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" |
| | :} |