NgsAdmixv2: Difference between revisions

From software
Jump to navigation Jump to search
 
(113 intermediate revisions by 2 users not shown)
Line 3: Line 3:


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.


[[File:NgsAdmix.png|thumb]]
[[File:NgsAdmix.png|thumb]]
Line 8: Line 10:
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]


=Citation=


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].
 
:'''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.
 
==Installation==
 
NGSadmix can be installed independently or as a part of ANGSD.


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
====NGSadmix Independent Installation====


<pre>
1. Login to your server using ssh on your terminal window.
Bibtex


% 24026093
2. Create the directory where you will install your software and enter it, such as
@Article{pmid24026093,
:<code>mkdir ~/Software</code>
  Author="Skotte, L. and Korneliussen, T. S.  and Albrechtsen, A. ",
:<code>cd ~/Software</code>
  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>


=Latest Version=
3. Download the source code:
The latest version is 32 from June 25 2013 and can be downloaded here: [http://popgen.dk/software/download/NGSadmix/ngsadmix32.cpp].
:<code>wget https://raw.githubusercontent.com/ANGSD/angsd/master/misc/ngsadmix32.cpp </code>


==Older Versions==
4. Configure, Compile and Install:
:<code>g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix</code>


Older versions can be found here:
====NGSadmix Installation from ANGSD====
[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=
:NGSadmix is part of the package ANGSD. To install ANGSD, please follow the instructions here [http://popgen.dk/angsd/index.php/Installation]


<pre>
==Parameters==


NGSadmix can be installed independently or as a part of ANGSD.
All parameters are set using '''-par value'''.
For example, to get additional information, you would write '''-printInfo 1'''.


1) NGSadmix Independent Installation:
<pre>./NGSadmix </pre>


Arguments:


Login to your server using ssh on your terminal window.
::'''-likes''' .beagle format filename with genotype likelihoods
Create the directory where you will install your software and enter it, such as
mkdir ~/Software
cd ~/Software


Download the source code:
::'''-K''' Number of ancestral populations
wget https://raw.githubusercontent.com/ANGSD/angsd/master/misc/ngsadmix32.cpp


Configure, Compile and Install:
Optional:
g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix


Delete source code to save space:
::'''-fname''' Ancestral population frequencies
rm ~/Software/ngsadmix32.cpp


::'''-qname''' Admixture proportions


::'''-outfiles''' Prefix for output files


</pre>
::'''-printInfo''' print ID and mean maximum allele frequency (maf) for the SNPs that were analysed


=Parameters=
Setup:


<div class="toccolours mw-collapsible mw-collapsed">
::'''-seed''' Seed for initial guess in EM algorithm (a number lower than 1M is preferred).
::  The same seed can be used to reproduce the analysis, and 3 different seeds can be used to test convergence.


./NGSadmix
::'''-P''' Number of threads
<pre class="mw-collapsible-content">


*** see doc for options/possible ranges/ and further explanation
::'''-method''' 0 indicates no acceleration of EM algorithm. Please refer to the paper for more information.


Arguments:
::'''-misTol''' Tolerance for considering a site as missing. Default = 0.05.
-likes .beagle format filename with genotype likelihoods
:: To include high quality genotypes only, increase this value (for example, 0.9)
-K Number of ancestral populations
Optional:
-fname Ancestral population frequencies
-qname Admixture proportions
-outfiles Prefix for output files
-printInfo print ID and mean maf for the SNPs that were analysed
Setup:
-seed Seed for initial guess in EM
-P Number of threads
-method If 0 no acceleration of EM algorithm
-misTol Tolerance for considering site as missing
Stop chriteria:
-tolLike50 Loglikelihood difference in 50 iterations
-tol Tolerance for convergence
-dymBound Use dymamic boundaries (1: yes (default) 0: no)
-maxiter Maximum number of EM iterations
Filtering
-minMaf Minimum minor allele frequency
-minLrt Minimum likelihood ratio value for maf>0
-minInd Minumum number of informative individuals
</pre>
</div>
NB All parameters are set using '''-par value'''. So to get additional information you would write '''-printInfo 1'''.


=Input Files=
Stop criteria:
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.
::'''-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
1_14000072      2      3      0.709    0.177    0.112    0.941    0.058    0.000    0.665    0.332    0.001
1_14000113      0      2      0.855    0.106    0.037    0.333    0.333    0.333    0.799    0.199    0.000
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.
 
You can also use bcftools' [https://samtools.github.io/bcftools/bcftools.html] 'query' option for generating a .beagle file from a .vcf file.
 
==Output Files==
The analysis performed by NGSadmix produces 4 files:
 
* 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.
 
* 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.
 
* 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.
 
==Run command example==


==Allele frequency ouput (.fopt)==
Download the input file, for example
Each column correponds to the estimated allele frequencies for each population and each line is a SNP
::<code>wget popgen.dk/software/download/NGSadmix/data/input.gz</code>
<div class="toccolours mw-collapsible mw-collapsed">
 
Example of a .fopt file for -K 3
Execute NGSadmix
<pre class="mw-collapsible-content">
::<code>./NGSadmix -likes input.gz -K 3 -P 4 -o myoutfiles -minMaf 0.05</code>
...
 
0.75331646167520038837 0.51190946588401886608 0.50134051056701267601
::* '''-likes''' Input .beagle file of genotype likelihoods = input.gz
0.99999999900000002828 0.80165850924934911603 0.97470665326916294813
::* '''-K''' Ancestral populations K=3
0.99999999900000002828 0.89560828888972687789 0.88062641752218895341
::* '''-P''' Number of threads used, as computer cores = 4
0.99999999900000002828 0.99999999900000002828 0.86109994249930577048
::* '''-o''' Output prefix, output file names = myoutfiles
0.70560445653074521655 0.78994686954000448154 0.93076614062025020413
::*'''-minMaf''' SNPs with MAF > 5% = 0.05
0.99999999900000002828 0.88878537780630872955 0.92662857068149151463
 
0.05322676762098016434 0.22871739860812340117 0.17394852600322696645
===Detailed Examples and Tutorial===
0.00000000100000000000 0.27428885137150410545 0.19029599645013275944
 
0.57086006389212373691 0.42232596591112880891 0.74080063581586474974
Please refer to the tutorial's page [http://www.popgen.dk/software/index.php/NgsAdmixTutorial]
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
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
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>


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"
:}

Latest revision as of 09:44, 12 July 2019

This page contains information about the program called NGSadmix, which is a very nice tool for estimating individual admixture proportions from NGS data. It is based on genotype likelihoods and works well for medium and low coverage NGS data. It is a fancy multithreaded c/c++ program which makes it useful for large datasets.

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.

The method was published in 2013 and can be found here: [1]


Software Download

The latest version of NGSadmix is ngsadmix32 from June 25, 2013 and can be downloaded here: [2].

Older Versions
The previous version of NGSadmix, ngsadmix31 can be found here: [3].
Version Log:
  • v32 june 25-2013; modified code such that it now compiles on OSX
  • v31 june 24-2013; First public version.

Installation

NGSadmix can be installed independently or as a part of ANGSD.

NGSadmix Independent Installation

1. Login to your server using ssh on your terminal window.

2. Create the directory where you will install your software and enter it, such as

mkdir ~/Software
cd ~/Software

3. Download the source code:

wget https://raw.githubusercontent.com/ANGSD/angsd/master/misc/ngsadmix32.cpp

4. Configure, Compile and Install:

g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix

NGSadmix Installation from ANGSD

NGSadmix is part of the package ANGSD. To install ANGSD, please follow the instructions here [4]

Parameters

All parameters are set using -par value. For example, to get additional information, you would write -printInfo 1.

./NGSadmix  

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 maximum allele frequency (maf) for the SNPs that were analysed

Setup:

-seed Seed for initial guess in EM algorithm (a number lower than 1M is preferred).
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:

-tolLike50 Loglikelihood difference in 50 iterations. Default= 0.1
-tol Tolerance for convergence. Default = 1x10-5. Use maller values for higher accuracy.
It's the maximum squared difference of F and Q (please refer to the paper for formula).
-dymBound Use dymamic boundaries (1: yes (default) 0: no).


-maxiter Maximum number of EM iterations. Default = 2000 (high value).
In case it doesn't converge, this value needs to be higher.

Filtering:

-minMaf Minimum minor allele frequency. Default = 5%
-minLrt Minimum likelihood ratio value for maf>0. Default = 0
-minInd Minumum number of informative individuals. Default = 0
It only keeps sites where there is at least x # of individuals with NGS data.

Input File

The input file contains genotype likelihoods in a .beagle file format [5]. 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 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 [6]

vcftools --vcf input.vcf --out test --BEAGLE-GL --chr 1,2

Chromosome has to be specified.

You can also use bcftools' [7] 'query' option for generating a .beagle file from a .vcf file.

Output Files

The analysis performed by NGSadmix produces 4 files:

  • 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.
  • 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.
  • 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.

Run command example

Download the input file, for example

wget popgen.dk/software/download/NGSadmix/data/input.gz

Execute NGSadmix

./NGSadmix -likes input.gz -K 3 -P 4 -o myoutfiles -minMaf 0.05
  • -likes Input .beagle file of genotype likelihoods = input.gz
  • -K Ancestral populations K=3
  • -P Number of threads used, as computer cores = 4
  • -o Output prefix, output file names = myoutfiles
  • -minMaf SNPs with MAF > 5% = 0.05

Detailed Examples and Tutorial

Please refer to the tutorial's page [8]

Citation

http://www.genetics.org/content/early/2013/09/03/genetics.113.154138.full.pdf

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

Bibtex
% 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"
}