NgsAdmixv2 - Revision history

Sonia4: /* Parameters */

2019-07-12T08:44:14Z

Parameters

← Older revision		Revision as of 10:44, 12 July 2019
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	::'''-seed''' Seed for initial guess in EM algorithm (a number lower than 1M is preferred).		::'''-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.		:: The same seed can be used to reproduce the analysis, and 3 different seeds can be used to test convergence.

	::'''-P''' Number of threads		::'''-P''' Number of threads
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	::'''-misTol''' Tolerance for considering a site as missing. Default = 0.05.		::'''-misTol''' Tolerance for considering a site as missing. Default = 0.05.
	::To include high quality genotypes only, increase this value (for example, 0.9)		:: To include high quality genotypes only, increase this value (for example, 0.9)

	Stop criteria:		Stop criteria:
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	::'''-tol''' Tolerance for convergence. Default = 1x10<sup>-5</sup>. Use maller values for higher accuracy.		::'''-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).		:: 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).		::'''-dymBound''' Use dymamic boundaries (1: yes (default) 0: no).
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	::'''-maxiter''' Maximum number of EM iterations. Default = 2000 (high value).		::'''-maxiter''' Maximum number of EM iterations. Default = 2000 (high value).
	::In case it doesn't converge, this value needs to be higher.		:: In case it doesn't converge, this value needs to be higher.

	Filtering:		Filtering:
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	::'''-minInd''' Minumum number of informative individuals. 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.		:: It only keeps sites where there is at least x # of individuals with NGS data.

	==Input File==		==Input File==

Sonia4 at 08:42, 12 July 2019

2019-07-12T08:42:31Z

← Older revision		Revision as of 10:42, 12 July 2019
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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]		:NGSadmix is part of the package ANGSD. To install ANGSD, please follow the instructions here [http://popgen.dk/angsd/index.php/Installation]

	~~==Quick start==~~
	~~:<code> ./NGSadmix -likes inputBeagleFile.gz -K 3 -o outFileName -P 10 </code>~~

	* '''-likes''' beagle file of genotype likelihoods
	* '''-K''' number of clusters
	* '''-o''' prefix of output file names
	* '''-P''' Number of threads used

	==Parameters==		==Parameters==
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	==Run command example==		==Run command example==

	Download the input file		Download the input file, for example
	::<code>wget popgen.dk/software/download/NGSadmix/data/input.gz</code>		::<code>wget popgen.dk/software/download/NGSadmix/data/input.gz</code>

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	::<code>./NGSadmix -likes input.gz -K 3 -P 4 -o myoutfiles -minMaf 0.05</code>		::<code>./NGSadmix -likes input.gz -K 3 -P 4 -o myoutfiles -minMaf 0.05</code>

	::Input file = input.gz		::* '''-likes''' Input .beagle file of genotype likelihoods = input.gz
	::Ancestral ~~Populations~~ K=3		::* '''-K''' Ancestral populations K=3
	::~~Computer~~ cores = 4 ~~(-P 4).~~		::* '''-P''' Number of threads used, as computer cores = 4
	::Output prefix = myoutfiles ~~(-o myoutfiles)~~		::* '''-o''' Output prefix, output file names = myoutfiles
	::SNPs with MAF > 5% ~~(-minMaf~~ 0.05)		::*'''-minMaf''' SNPs with MAF > 5% = 0.05

	===Detailed Examples and Tutorial===		===Detailed Examples and Tutorial===

Albrecht: /* Input File */

2019-07-12T07:49:10Z

Input File

← Older revision		Revision as of 09:49, 12 July 2019
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	The input file contains genotype likelihoods in a .beagle file format [http://faculty.washington.edu/browning/beagle/beagle.html].		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.		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]

			<pre>
			vcftools --vcf input.vcf --out test --BEAGLE-GL --chr 1,2
			</pre>
			Chromosome has to be specified.

	~~We recommend using~~ [~~[ANGSD]] for easy transformation of Next-generation sequencing data to .beagle format. Please~~		You can also use bcftools' [https://samtools.github.io/bcftools/bcftools.html] 'query' option for generating a .beagle file from a .vcf file.
	~~see [http~~://~~www~~.~~popgen~~.dk/~~angsd~~/~~index~~.~~php/Beagle_input Creation of Beagle files with ANGSD~~]

	==Output Files==		==Output Files==

Albrecht: /* Parameters */

2019-07-12T07:36:26Z

Parameters

← Older revision		Revision as of 09:36, 12 July 2019
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	For example, to get additional information, you would write '''-printInfo 1'''.		For example, to get additional information, you would write '''-printInfo 1'''.

	./NGSadmix		<pre>./NGSadmix </pre>

	Arguments:		Arguments:

Albrecht: /* Parameters */

2019-07-12T07:35:59Z

Parameters

← Older revision		Revision as of 09:35, 12 July 2019
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	::'''-dymBound''' Use dymamic boundaries (1: yes (default) 0: no).		::'''-dymBound''' Use dymamic boundaries (1: yes (default) 0: no).
	~~'''''ANDERS: If used as default (yes), it allows low F and Q values in the first 50 iterations. ANDERS'''''~~

	::'''-maxiter''' Maximum number of EM iterations. Default = 2000 (high value).		::'''-maxiter''' Maximum number of EM iterations. Default = 2000 (high value).

Albrecht: /* Quick start */

2019-07-12T07:35:46Z

Quick start

← Older revision		Revision as of 09:35, 12 July 2019
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	==Quick start==		==Quick start==
	:<code> ./NGSadmix -likes inputBeagleFile.gz -K 3 </code>		:<code> ./NGSadmix -likes inputBeagleFile.gz -K 3 -o outFileName -P 10 </code>

			* '''-likes''' beagle file of genotype likelihoods
			* '''-K''' number of clusters
			* '''-o''' prefix of output file names
			* '''-P''' Number of threads used

	==Parameters==		==Parameters==

Albrecht at 07:32, 12 July 2019

2019-07-12T07:32:25Z

← Older revision		Revision as of 09:32, 12 July 2019
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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]		:NGSadmix is part of the package ANGSD. To install ANGSD, please follow the instructions here [http://popgen.dk/angsd/index.php/Installation]

			==Quick start==
			:<code> ./NGSadmix -likes inputBeagleFile.gz -K 3 </code>
	==Parameters==		==Parameters==

Albrecht: /* NGSadmix Independent Installation */

2019-07-12T07:30:38Z

NGSadmix Independent Installation

← Older revision		Revision as of 09:30, 12 July 2019
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	4. Configure, Compile and Install:		4. Configure, Compile and Install:
	:<code>g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix</code>		:<code>g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix</code>

	~~5. Delete source code to save space:~~
	~~:<code>rm ~/Software/ngsadmix32.cpp</code>~~


	====NGSadmix Installation from ANGSD====		====NGSadmix Installation from ANGSD====

Sonia4: /* Run command example */

2019-07-11T20:24:37Z

Run command example

← Older revision		Revision as of 22:24, 11 July 2019
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	::Output prefix = myoutfiles (-o myoutfiles)		::Output prefix = myoutfiles (-o myoutfiles)
	::SNPs with MAF > 5% (-minMaf 0.05)		::SNPs with MAF > 5% (-minMaf 0.05)


	===Detailed Examples and Tutorial===		===Detailed Examples and Tutorial===

	Please refer to the tutorial's page [http://www.popgen.dk/software/index.php/NgsAdmixTutorial]		Please refer to the tutorial's page [http://www.popgen.dk/software/index.php/NgsAdmixTutorial]


	==Citation==		==Citation==

Sonia4 at 20:24, 11 July 2019

2019-07-11T20:24:10Z

← Older revision		Revision as of 22:24, 11 July 2019
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	* 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.		* 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==		==Run command example==